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Another image that might be familiar to some of you working with Python can be found on [xkcd - superfund](https://xkcd.com/1987/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Demo + +``````{challenge} Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +Answer in the collaborative document: + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} Dependencies-2: Create a time-capsule for the future +Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + Try this either with your own project or inside the "coderefinery" conda + environment: + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ conda env create -f environment.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` + + +```{keypoints} +- Recording dependencies with versions can make it easier for the next person to execute your code +- There are many tools to record dependencies +``` \ No newline at end of file diff --git a/_sources/environments.md.txt b/_sources/environments.md.txt new file mode 100644 index 0000000..e36045f --- /dev/null +++ b/_sources/environments.md.txt @@ -0,0 +1,286 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 10 min demo +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**. + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +## You may have use for containers in different ways + +- Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead! +- You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container! + - If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough. + +## The container recipe + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + +````{exercise} (optional) Containers-2: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` + +## Resources for further learning + +- [Carpentries incubator lesson on Docker](https://carpentries-incubator.github.io/docker-introduction/) +- [Carpentries incubator lesson on Singularity/Apptainer](https://carpentries-incubator.github.io/singularity-introduction/) + + +```{keypoints} +- Containers can be helpful if complex setups are needed to running a specific software +- They can also be helpful for prototyping without "messing up" your own computing environment, or for running software that requires a different operating system than your own +``` diff --git a/_sources/exercises.md.txt b/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/_sources/guide.md.txt b/_sources/guide.md.txt new file mode 100644 index 0000000..97261f0 --- /dev/null +++ b/_sources/guide.md.txt @@ -0,0 +1,155 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +Two example schedules for this lesson: + +This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Overview of CR and how it all fits together +- 09:10 - 09:20 Reproducible research, [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:27 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:27 - 09:35 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) - discussion +- 09:35 - 10:00 Snakemake exercise (25 min) +- 10:00 - 10:10 Break +- 10:10 - 10:15 Summary of workflows and the exercise +- 10:15 - 10:30 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- 10:30 - 10:40 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) +- 10:40 - 11:00 Container-1 exercise (20 min) +- 11:00 - 11.05 Wrapup + +This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break): + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..05828e6 --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,57 @@ +.. _index: + +Reproducible research - Preparing code to be usable by you and others in the future +=================================================================================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves and others. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - Be able to apply well organized directory structure for their project + - Understand that code can have dependencies, and know how to document them + - Be able to document computational steps, and have an idea when it can be useful + - Know about use cases for containers + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + intro.md + motivation.md + organizing-projects.md + workflow-management.md + dependencies.md + environments.md + where-to-go.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/_sources/intro.md.txt b/_sources/intro.md.txt new file mode 100644 index 0000000..6690f38 --- /dev/null +++ b/_sources/intro.md.txt @@ -0,0 +1,16 @@ +# Introduction - How it all connects + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +--- + +```{figure} img/reproducible_research_plus_lessons.png +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, ] + diff --git a/_sources/motivation.md.txt b/_sources/motivation.md.txt new file mode 100644 index 0000000..07d1f8e --- /dev/null +++ b/_sources/motivation.md.txt @@ -0,0 +1,74 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[Steeves, Vicky (2017) in "Reproducibility Librarianship," Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4] + +This also means that you can think about it from the beginning of your research life cycle! + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` + +```{keypoints} +- Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch +``` \ No newline at end of file diff --git a/_sources/organizing-projects.md.txt b/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..c46ad19 --- /dev/null +++ b/_sources/organizing-projects.md.txt @@ -0,0 +1,120 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the first steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* Check the [Git-intro lesson](https://coderefinery.github.io/git-intro/) for a reminder. + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in the collaborative document: + +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on the fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +## Some tools and templates + +- [R devtools](https://devtools.r-lib.org/) +- [Python cookiecutter template](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) +- [Reproducible research template](https://github.com/the-turing-way/reproducible-project-template) by the Turing Way + +More tools and templates in [Heidi Seibolds blog](https://heidiseibold.ck.page/posts/setting-up-a-fair-and-reproducible-project). + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration: + - [Overleaf](https://www.overleaf.com) or [Typst](https://typst.app/): online, collaborative LaTeX editor + - [Authorea](https://www.authorea.com): collaborative platform for preprints + - [HackMD](https://hackmd.io/) or [HedgeDoc](https://hedgedoc.org/): online collaborative Markdown editors + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as, see also our [Jupyter lesson](https://coderefinery.github.io/jupyter/) later in this workshop. + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + +```{keypoints} +- An organized project directory structure helps with reproducibility. +``` diff --git a/_sources/where-to-go.md.txt b/_sources/where-to-go.md.txt new file mode 100644 index 0000000..b524992 --- /dev/null +++ b/_sources/where-to-go.md.txt @@ -0,0 +1,53 @@ +# Where to go from here + +```{objectives} +- Understand when tools discussed in this episode can be useful +``` + +```{instructor-note} +- 10 min teaching/discussion +``` + +This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project. + +## Important for every project + +* Clear file structure for your project +* At least consider the possibility that someone, maybe you may want to reproduce your work + * Can you do something (small) to make it easier? + * If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help. + +## Workflow tools will maybe make sense in the future + +* In many cases, it is probably not needed +* You will want to consider workflow tools: + * When processing many files with many steps + * Steps or files may change + * Your main script, connecting your steps gets very long + * ... + +## When should I worry about dependencies? + +* Your code depends on multiple other packages +* You want to avoid questions like: "What do I need to install to run your code" +* You want help yourself running your code + * After a few years + * On a different computer + * ... + +## Containers seem amazing, but do I have use for them? + +* Maybe not yet, but knowing that you can ... + * Run Linux tools on your Windows computer + * Run different versions of same software on your computer + * Follow the "easy installation instructions" for an operating system that is not your own + * Get a fully configured environment instead of only installing a tool + * Share your setup and configurations with others +... can be very beneficial :) + + +```{keypoints} +- Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution. +- Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/_sources/workflow-management.md.txt b/_sources/workflow-management.md.txt new file mode 100644 index 0000000..83caaf6 --- /dev/null +++ b/_sources/workflow-management.md.txt @@ -0,0 +1,241 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 5 min teaching +- 15 min demo +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: + +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps. + +Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But **imagine having 4 steps and 500 books**. +How could we deal with this? + +As a first idea we could express the workflow with a script. The repository includes such script called `run_all.sh`. + +We can run it with: + +```console +$ bash run_all.sh +``` + +This is **imperative style**: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another. + +````{discussion} +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + + ```{solution} + The advantage of this solution compared to processing one by one is more automation: We can generate all. + This is not only easier, it is also less error-prone. + + Yes, the scripted solution can be reproducible. But could you easily run it e.g. on a Windows computer? + + If we had more steps and once steps start to be time-consuming, a limitation of + a scripted solution is that it tries to run all steps always. Rerunning only + part of the steps or only part of the input data requires us to outcomment or change lines in our script in between runs which can again become tedious and error-prone. + ``` +```` + +--- + +## Workflow tools + +Sometimes it may be helpful to go from imperative to declarative style. Rather than saying "do this and then that" we describe dependencies but we let the tool figure out the series of steps to produce results. + +### Example workflow tool: [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) + +Snakemake (inspired by [GNU Make](https://www.gnu.org/software/make/)) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition. + +--- + +## A demo + +````{prereq} Preparation +The exercise (below) and pre-exercise discussion uses the +word-count repository +() which we need to clone to work on it. + +If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the [CodeRefinery installation instruction page](https://coderefinery.github.io/installation/)), or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Install the necessary tools +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution in the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='code/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='code/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' + +``` + +We can see that Snakemake uses **declarative style**: +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Steps: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containing "shell". +``` +```` + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle **learning curve**. +- Free, open-source, and **installs easily** via conda or pip. +- **Cross-platform** (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them **in parallel**. +- Is is possible to define **isolated software environments** per rule, e.g. by adding `conda: 'environment.yml'` to a rule. +- Also possible to run workflows in Docker or Apptainer **containers** e.g. by adding `container: 'docker://some-org/some-tool#2.3.1'` to a rule. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is **completely general**. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + +Tools like Snakemake help us with **reproducibility** by supporting us with **automation**, **scalability** and **portability** of our workflows. + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. +- [Book on building reproducible analytical pipelines with R](https://raps-with-r.dev/) + +```{keypoints} +- Computational steps can be recorded in many ways +- Workflow tools can help, if there are many steps to be executed +``` diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/_static/check-solid.svg b/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/_static/clipboard.min.js b/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/_static/copybutton.css b/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/_static/copybutton.js b/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/_static/copybutton_funcs.js b/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/_static/css/badge_only.css @@ -0,0 +1 @@ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight 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score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/sphinx_lesson.css b/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/_static/sphinx_rtd_theme_ext_color_contrast.css b/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/_static/tabs.css b/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/_static/tabs.js b/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/_static/term_role_formatting.css b/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/_static/togglebutton.css b/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/_static/togglebutton.js b/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
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+``` + +```{instructor-note} +- 10 min teaching +- 20 min exercises +``` +Our codes often depend on other codes that in turn depend on other codes ... + +- **Reproducibility**: We can version-control our code with Git but how should we version-control dependencies? + How can we capture and communicate dependencies? +- **Dependency hell**: Different codes on the same environment can have conflicting dependencies. + +```{figure} img/python_environment.png +:alt: Python environment +:width: 60% + +From [xkcd](https://xkcd.com/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Exercises + +``````{challenge} Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} Dependencies-2: Create a time-capsule for the future +Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + Try this either with your own project or inside the "coderefinery" conda + environment: + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ conda env create -f environment.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` diff --git a/branch/citation/_sources/environments.md.txt b/branch/citation/_sources/environments.md.txt new file mode 100644 index 0000000..0249dd8 --- /dev/null +++ b/branch/citation/_sources/environments.md.txt @@ -0,0 +1,267 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 20 min exercise +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**, + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + +````{exercise} Containers-2: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` diff --git a/branch/citation/_sources/exercises.md.txt b/branch/citation/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/branch/citation/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/branch/citation/_sources/guide.md.txt b/branch/citation/_sources/guide.md.txt new file mode 100644 index 0000000..941449a --- /dev/null +++ b/branch/citation/_sources/guide.md.txt @@ -0,0 +1,149 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +This was the schedule at our last workshop: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Many participants do not share data or code, and in particular they are often +unaware that research output other than published articles can be assigned +digital object identifiers (DOIs). +The "Sharing code and data" is meant to bring awareness about FAIRness and Open Science +and to show how DOIs can be obtained for Git repositories.. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +#### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + +Perhaps we shouldn't have done the Zenodo example - we could do a +quick demo, but because of limited time, I'm not sure if it conveyed +how cool it was. Maybe we should have simply said it. Alternatively, +we could have not done the Docker demonstration and given more time +for Zenodo. diff --git a/branch/citation/_sources/index.rst.txt b/branch/citation/_sources/index.rst.txt new file mode 100644 index 0000000..266d52f --- /dev/null +++ b/branch/citation/_sources/index.rst.txt @@ -0,0 +1,60 @@ +.. _index: + +Reproducible research +===================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - be able to apply well organized directory structure for their project + - remember the FAIR principles + - understand that code can have dependencies, and know how to document them + - if a computational studies contains several steps, be able to document them + - know about use cases for containers + - knowing the pros and cons of manual documentation vs. scripted automation vs. workflow management + - be able to create a DOI for research output like code or data + + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + motivation.md + organizing-projects.md + dependencies.md + workflow-management.md + environments.md + sharing.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/branch/citation/_sources/motivation.md.txt b/branch/citation/_sources/motivation.md.txt new file mode 100644 index 0000000..9045eec --- /dev/null +++ b/branch/citation/_sources/motivation.md.txt @@ -0,0 +1,77 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[citation needed] + +--- + +```{figure} img/reproducible-research.jpg +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs - figure by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Heidi Seibold, CC-BY 4.0, ] + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` diff --git a/branch/citation/_sources/organizing-projects.md.txt b/branch/citation/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..ec474a9 --- /dev/null +++ b/branch/citation/_sources/organizing-projects.md.txt @@ -0,0 +1,125 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the most basic steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* We went over all of this in [Git-intro](https://coderefinery.github.io/git-intro/) + +--- + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist: + - [Overleaf](https://www.overleaf.com): an online, collaborative LaTeX editor (has Git integration) + - [Authorea](https://www.authorea.com): collaborative platform for preprints (apparently also has Git integration) + - [HackMD](https://hackmd.io/): an online collaborative Markdown editor (has Git integration) + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in collaborative document or with your team members +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on yhe fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +````{discussion} Discuss in collaborative document or with your team members +``` +- What tools are you using when organizing your projects? + - ... + - ... + - (share your experience) +``` +```` + + +```{keypoints} +- An organized project directory structure helps with reproducibility. +- Reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/branch/citation/_sources/sharing.md.txt b/branch/citation/_sources/sharing.md.txt new file mode 100644 index 0000000..9993561 --- /dev/null +++ b/branch/citation/_sources/sharing.md.txt @@ -0,0 +1,199 @@ +# Sharing code and data + + +```{questions} +- How can I share research code and data? +``` + +```{objectives} +- Discuss the pros and cons of open science +- Learn how to mint a DOI for your project +``` + +```{instructor-note} +- 10 min teaching +- 15 min exercises +``` +--- + +## Sharing research data + +The Open Science movement encourages researchers +to share research output beyond the contents of a +published academic article (and possibly supplementary information). + +```{figure} img/Open_Science_Principles.png +:alt: Research comic +:width: 90% +``` + +Arguments in favor [(from Wikipedia)](https://en.wikipedia.org/wiki/Open_science): +- Open access publication of research reports and data allows for rigorous peer-review +- Science is publicly funded so all results of the research should be publicly available +- Open Science will make science more reproducible and transparent +- Open Science has more impact +- Open Science will help answer uniquely complex questions + +Arguments against [(from Wikipedia)](https://en.wikipedia.org/wiki/Open_science): +- Too much unsorted information overwhelms scientists +- Potential misuse +- The public will misunderstand science data +- Increasing the scale of science will make verification of any discovery more difficult +- Low-quality science + +```{figure} img/turing-way/36-data-research-cycle.jpg +:alt: Research comic +:width: 100% +``` + +(This image was created by [Scriberia](http://www.scriberia.co.uk) for [The +Turing Way](https://the-turing-way.netlify.com) community and is used under a +CC-BY licence. The image was obtained from [https://zenodo.org/record/3332808](https://zenodo.org/record/3332808).) + +--- + +## FAIR principles + +```{figure} img/turing-way/8-fair-principles.jpg +:alt: Research comic +:width: 100% +``` + +(This image was created by [Scriberia](http://www.scriberia.co.uk) for [The +Turing Way](https://the-turing-way.netlify.com) community and is used under a +CC-BY licence. The image was obtained from [https://zenodo.org/record/3332808](https://zenodo.org/record/3332808).) + +"FAIR" is the current buzzword for data management. You may be asked +about it in, for example, making data management plans for grants: + +- **F**indable + - Will anyone else know that your data exists? + - Solutions: put it in a standard repository, or at least a + description of the data. Get a digital object identifier (DOI). +- **A**ccessible + - Once someone knows that the data exists, can they get it? + - Usually solved by being in a repository, but for non-open data, + may require more procedures. +- **I**nteroperable + - Is your data in a format that can be used by others, like csv + instead of PDF? + - Or better than csv. Example: [5-star open data](https://5stardata.info/en/) +- **R**eusable + - Is there a license allowing others to re-use? + +Even though this is usually referred to as "open data", it means +considering and making good decisions, even if non-open. + +FAIR principles are usually discussed in the context of data, +but they apply also for research software. + +Note that FAIR principles do not require data/software to be open. + +```{discussion} Discuss open science +- Do you share any other research outputs besides published articles and possibly source code? +- Discuss pros and cons of sharing research data. +``` + +--- + +## Exercise - Connecting repositories to Zenodo + +```{exercise} Sharing-1: Get a DOI from Zenodo +Digital object identifiers (DOI) are the backbone of the academic +reference and metrics system. In this exercise we will see how to +make a GitHub repository citable by archiving it on the +[Zenodo](http://about.zenodo.org/) archiving service. Zenodo is a +general-purpose open access repository created by OpenAIRE and CERN. + +1. Sign in to Zenodo using your GitHub account. For this exercise, use the + sandbox service: [https://sandbox.zenodo.org/login/](https://sandbox.zenodo.org/login/). This is a test version of the real Zenodo platform. +2. Go to [https://sandbox.zenodo.org/account/settings/github/](https://sandbox.zenodo.org/account/settings/github/). +3. Find the repository you wish to publish, + and flip the switch to ON. +4. Go to GitHub and create a **release** by clicking the `Create a new release` on the + right-hand side (a release is based on a Git tag, but is a higher-level GitHub feature). + You will need to enter a tag name (e.g. v0.1) in the "Choose a tag" box. +5. Creating a new release will trigger Zenodo into archiving your repository, + and a DOI badge will be displayed next to your repository after a minute + or two. You can include it in your GitHub README file: click the + DOI badge and copy the relevant format (Markdown, RST, HTML). +``` + +--- + +## Services for sharing and collaborating on research data + +To find a research data repository for your data, you can search on the +[Registry of Research Data Repositories (re3data)](https://www.re3data.org/) +platform and filter by country, content type, discipline, etc. + +**International:** + +- [Zenodo](https://zenodo.org/): A general-purpose open access repository + created by OpenAIRE and CERN. Integration with GitHub, allows + researchers to upload files up to 50 GB. +- [Figshare](https://figshare.com/): Online digital repository where researchers + can preserve and share their research outputs (figures, datasets, images and videos). + Users can make all of their research outputs available in a citable, + shareable and discoverable manner. +- [EUDAT](https://eudat.eu): European platform for researchers and practitioners from any research discipline to preserve, find, access, and process data in a trusted environment. +- [Dryad](https://datadryad.org/): A general-purpose home for a wide diversity of datatypes, + governed by a nonprofit membership organization. + A curated resource that makes the data underlying scientific publications discoverable, + freely reusable, and citable. +- [The Open Science Framework](https://osf.io/): Gives free accounts for collaboration + around files and other research artifacts. Each account can have up to 5 GB of files + without any problem, and it remains private until you make it public. + +**Sweden:** + +- [ICOS for climate data](http://www.icos-sweden.se/) +- [Bolin center climate / geodata](https://bolin.su.se/data/) +- [NBIS for life science, sequence –omics data](https://nbis.se/infrastructure) + +**Norway:** + +- [NIRD archive is widely used by some communities](https://archive.norstore.no/) +- [NSD - Norwegian Center for Research Data, for any kind of data](https://nsd.no/nsd/english/index.html) +- [Dataverse.no - Dataverse network, based at University of Tromsø but open for other institutions](https://dataverse.no/) + +**Denmark:** + +- [opendata.dk nationwide portal](http://www.opendata.dk) +- [Danish portal for sharing geographical data](http://brugstedet.dk/) + +**Finland:** + +- [IDA, for general data](https://ida.fairdata.fi/login) +- [FSD for social data](https://www.fsd.uta.fi/en/) +- [more information on Finnish resources for open data](https://www.fairdata.fi/en/) + +--- + +## Resources for data management + +- [DataLad](https://www.datalad.org/) +- [Data Stewardship Wizard](https://ds-wizard.org/) + +--- + +## Further reading on reproducibility and open science + +- [The Turing way](https://github.com/alan-turing-institute/the-turing-way/) +- [Illustrations from the Turing Way book dashes](https://zenodo.org/record/3332808) +- [Reproduciblity syllabus](http://lorenabarba.com/blog/barbagroup-reproducibility-syllabus/) +- The [reproducible research data analysis platform](http://www.reana.io/) +- Good talks on open reproducible research can be found [here](http://inundata.org/talks/index.html). +- ["FAIR is not fair enough"](https://danielskatzblog.wordpress.com/2017/06/22/fair-is-not-fair-enough/) +- ["A FAIRer future"](https://www.nature.com/articles/s41567-019-0624-3) +- ["Top 10 FAIR Data & Software Things"](https://librarycarpentry.org/Top-10-FAIR/) are brief guides that can be used by the research community to understand how they can make their research (data and software) more FAIR. +- [Five recommendations for fair software](https://fair-software.eu/) +- [Publishing research software](https://libguides.mit.edu/software) A MIT libraries webpage on why to publish software, where to publish software, and how to make software citable. +- [Software Quality Checklist](https://technical-reference.readthedocs.io/en/latest/quality/software-checklist.html) +- [MolSSI Best Practice Guides](http://molssi.org/education/best-practices/) +- [Five recommendations for fair software](https://fair-software.eu/) +- [Awesome Research Software Registries](https://github.com/NLeSC/awesome-research-software-registries) + +```{keypoints} +- Consider sharing other research outputs than articles. +``` diff --git a/branch/citation/_sources/workflow-management.md.txt b/branch/citation/_sources/workflow-management.md.txt new file mode 100644 index 0000000..5093c3d --- /dev/null +++ b/branch/citation/_sources/workflow-management.md.txt @@ -0,0 +1,253 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 10 min teaching +- 20 min exercises +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +```{discussion} +We have two steps and 4 books. But **imagine having 4 steps and processing 500 books**. +Can you relate? Are you using similar setups in your research? How do you record them? +``` + +````{discussion} Kitchen analogy +```{figure} img/kitchen/busy.png +:alt: Busy kitchen +:width: 50% + +Now we have many similar meals to prepare and possibly many chefs +present (cores) and workflow tools can help us to plan and document the steps +and run them efficiently. [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Exercise + +````{prereq} Exercise preparation +The exercise (below) and pre-exercise discussion uses a simple +word-count repository +(). We should clone the +repository already to prepare to work on it. + +You could do the exercise either on your own computer, or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Scripted solution for processing 4 books +Somebody wrote a script (`script.sh`) to process all 4 books: + +```{code-block} bash +--- +emphasize-lines: 4 +--- + +#!/usr/bin/env bash + +# loop over all books +for title in abyss isles last sierra; do + python statistics/count.py data/${title}.txt > statistics/${title}.data + python plot/plot.py --data-file statistics/${title}.data --plot-file plot/${title}.png +done +``` + +We can run it with: +```console +$ bash script.sh +``` + +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + +```{solution} +The advantage of this solution compared to processing one by one is more automation: We can generate all. +This is not only easier, it is also less error-prone. + +Yes, the scripted solution can be reproducible. + +If we had more steps and once steps start to be time-consuming, a limitation of +a scripted solution is that it tries to run all steps always. Rerunning only +part of the steps or only part of the input data requires us to outcomment +lines in our script which can again become tedious and error-prone. +``` +```` + +````{exercise} Workflow-2: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution +and the interesting file here is the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='statistics/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + conda: 'environment.yml' + log: 'statistics/{file}.log' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='plot/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + conda: 'environment.yml' + log: 'plot/{file}.log' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' +``` + +Snakemake uses **declarative style**: we describe dependencies but we let +Snakemake figure out the series of steps to produce results (targets). +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Exercise goals: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containeing "shell". +``` +```` + + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle learning curve. +- Free, open-source, and installs easily via conda or pip. +- Cross-platform (Windows, MacOS, Linux) and compatible with all HPC schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is completely general. +- Is is possible to define isolated software environments per rule, see [here](https://github.com/coderefinery/word-count/blob/f4ca47440751dd2c65f55fef1a8d9f181ecdd2f6/Snakefile#L15). +- Also possible to run workflows in Docker or Apptainer containers. +- Workflows can be pushed out to run on a cluster or in the cloud without modifications to scale up. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. + + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`). It's not necessary to +run this step yourself. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` diff --git a/branch/citation/_static/_sphinx_javascript_frameworks_compat.js b/branch/citation/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8549469 --- /dev/null +++ b/branch/citation/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,134 @@ +/* + * _sphinx_javascript_frameworks_compat.js + * ~~~~~~~~~~ + * + * Compatability shim for jQuery and underscores.js. + * + * WILL BE REMOVED IN Sphinx 6.0 + * xref RemovedInSphinx60Warning + * + */ + +/** + * select a different prefix for underscore + */ +$u = _.noConflict(); + + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/citation/_static/basic.css b/branch/citation/_static/basic.css new file mode 100644 index 0000000..4e9a9f1 --- /dev/null +++ b/branch/citation/_static/basic.css @@ -0,0 +1,900 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; 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+} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/citation/_static/check-solid.svg b/branch/citation/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/citation/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/citation/_static/clipboard.min.js b/branch/citation/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/citation/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/citation/_static/copybutton.css b/branch/citation/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/citation/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/citation/_static/copybutton.js b/branch/citation/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/citation/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/citation/_static/copybutton_funcs.js b/branch/citation/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/citation/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/citation/_static/css/badge_only.css b/branch/citation/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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--- /dev/null +++ b/branch/citation/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/branch/citation/_static/documentation_options.js b/branch/citation/_static/documentation_options.js new file mode 100644 index 0000000..c066c69 --- /dev/null +++ b/branch/citation/_static/documentation_options.js @@ -0,0 +1,14 @@ +var DOCUMENTATION_OPTIONS = { + URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), + VERSION: '', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'dirhtml', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/branch/citation/_static/file.png b/branch/citation/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/branch/citation/_static/file.png differ diff --git a/branch/citation/_static/jquery-3.6.0.js b/branch/citation/_static/jquery-3.6.0.js new file mode 100644 index 0000000..fc6c299 --- /dev/null +++ b/branch/citation/_static/jquery-3.6.0.js @@ -0,0 +1,10881 @@ +/*! + * jQuery JavaScript Library v3.6.0 + * https://jquery.com/ + * + * Includes Sizzle.js + * https://sizzlejs.com/ + * + * Copyright OpenJS Foundation and other contributors + * Released under the MIT license + * https://jquery.org/license + * + * Date: 2021-03-02T17:08Z + */ +( function( global, factory ) { + + "use strict"; + + if ( typeof module === "object" && typeof module.exports === "object" ) { + + // For CommonJS and CommonJS-like environments where a proper `window` + // is present, execute the factory and get jQuery. + // For environments that do not have a `window` with a `document` + // (such as Node.js), expose a factory as module.exports. + // This accentuates the need for the creation of a real `window`. + // e.g. var jQuery = require("jquery")(window); + // See ticket #14549 for more info. + module.exports = global.document ? + factory( global, true ) : + function( w ) { + if ( !w.document ) { + throw new Error( "jQuery requires a window with a document" ); + } + return factory( w ); + }; + } else { + factory( global ); + } + +// Pass this if window is not defined yet +} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { + +// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 +// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode +// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common +// enough that all such attempts are guarded in a try block. +"use strict"; + +var arr = []; + +var getProto = Object.getPrototypeOf; + +var slice = arr.slice; + +var flat = arr.flat ? function( array ) { + return arr.flat.call( array ); +} : function( array ) { + return arr.concat.apply( [], array ); +}; + + +var push = arr.push; + +var indexOf = arr.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var fnToString = hasOwn.toString; + +var ObjectFunctionString = fnToString.call( Object ); + +var support = {}; + +var isFunction = function isFunction( obj ) { + + // Support: Chrome <=57, Firefox <=52 + // In some browsers, typeof returns "function" for HTML elements + // (i.e., `typeof document.createElement( "object" ) === "function"`). + // We don't want to classify *any* DOM node as a function. + // Support: QtWeb <=3.8.5, WebKit <=534.34, wkhtmltopdf tool <=0.12.5 + // Plus for old WebKit, typeof returns "function" for HTML collections + // (e.g., `typeof document.getElementsByTagName("div") === "function"`). (gh-4756) + return typeof obj === "function" && typeof obj.nodeType !== "number" && + typeof obj.item !== "function"; + }; + + +var isWindow = function isWindow( obj ) { + return obj != null && obj === obj.window; + }; + + +var document = window.document; + + + + var preservedScriptAttributes = { + type: true, + src: true, + nonce: true, + noModule: true + }; + + function DOMEval( code, node, doc ) { + doc = doc || document; + + var i, val, + script = doc.createElement( "script" ); + + script.text = code; + if ( node ) { + for ( i in preservedScriptAttributes ) { + + // Support: Firefox 64+, Edge 18+ + // Some browsers don't support the "nonce" property on scripts. + // On the other hand, just using `getAttribute` is not enough as + // the `nonce` attribute is reset to an empty string whenever it + // becomes browsing-context connected. + // See https://github.com/whatwg/html/issues/2369 + // See https://html.spec.whatwg.org/#nonce-attributes + // The `node.getAttribute` check was added for the sake of + // `jQuery.globalEval` so that it can fake a nonce-containing node + // via an object. + val = node[ i ] || node.getAttribute && node.getAttribute( i ); + if ( val ) { + script.setAttribute( i, val ); + } + } + } + doc.head.appendChild( script ).parentNode.removeChild( script ); + } + + +function toType( obj ) { + if ( obj == null ) { + return obj + ""; + } + + // Support: Android <=2.3 only (functionish RegExp) + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call( obj ) ] || "object" : + typeof obj; +} +/* global Symbol */ +// Defining this global in .eslintrc.json would create a danger of using the global +// unguarded in another place, it seems safer to define global only for this module + + + +var + version = "3.6.0", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }; + +jQuery.fn = jQuery.prototype = { + + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + + // Return all the elements in a clean array + if ( num == null ) { + return slice.call( this ); + } + + // Return just the one element from the set + return num < 0 ? this[ num + this.length ] : this[ num ]; + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + each: function( callback ) { + return jQuery.each( this, callback ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map( this, function( elem, i ) { + return callback.call( elem, i, elem ); + } ) ); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + even: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return ( i + 1 ) % 2; + } ) ); + }, + + odd: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return i % 2; + } ) ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: arr.sort, + splice: arr.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var options, name, src, copy, copyIsArray, clone, + target = arguments[ 0 ] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // Skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !isFunction( target ) ) { + target = {}; + } + + // Extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + + // Only deal with non-null/undefined values + if ( ( options = arguments[ i ] ) != null ) { + + // Extend the base object + for ( name in options ) { + copy = options[ name ]; + + // Prevent Object.prototype pollution + // Prevent never-ending loop + if ( name === "__proto__" || target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject( copy ) || + ( copyIsArray = Array.isArray( copy ) ) ) ) { + src = target[ name ]; + + // Ensure proper type for the source value + if ( copyIsArray && !Array.isArray( src ) ) { + clone = []; + } else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) { + clone = {}; + } else { + clone = src; + } + copyIsArray = false; + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend( { + + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + isPlainObject: function( obj ) { + var proto, Ctor; + + // Detect obvious negatives + // Use toString instead of jQuery.type to catch host objects + if ( !obj || toString.call( obj ) !== "[object Object]" ) { + return false; + } + + proto = getProto( obj ); + + // Objects with no prototype (e.g., `Object.create( null )`) are plain + if ( !proto ) { + return true; + } + + // Objects with prototype are plain iff they were constructed by a global Object function + Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; + return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; + }, + + isEmptyObject: function( obj ) { + var name; + + for ( name in obj ) { + return false; + } + return true; + }, + + // Evaluates a script in a provided context; falls back to the global one + // if not specified. + globalEval: function( code, options, doc ) { + DOMEval( code, { nonce: options && options.nonce }, doc ); + }, + + each: function( obj, callback ) { + var length, i = 0; + + if ( isArrayLike( obj ) ) { + length = obj.length; + for ( ; i < length; i++ ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } else { + for ( i in obj ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } + + return obj; + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArrayLike( Object( arr ) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + return arr == null ? -1 : indexOf.call( arr, elem, i ); + }, + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + for ( ; j < len; j++ ) { + first[ i++ ] = second[ j ]; + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var length, value, + i = 0, + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArrayLike( elems ) ) { + length = elems.length; + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return flat( ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +} ); + +if ( typeof Symbol === "function" ) { + jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; +} + +// Populate the class2type map +jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), + function( _i, name ) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); + } ); + +function isArrayLike( obj ) { + + // Support: real iOS 8.2 only (not reproducible in simulator) + // `in` check used to prevent JIT error (gh-2145) + // hasOwn isn't used here due to false negatives + // regarding Nodelist length in IE + var length = !!obj && "length" in obj && obj.length, + type = toType( obj ); + + if ( isFunction( obj ) || isWindow( obj ) ) { + return false; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v2.3.6 + * https://sizzlejs.com/ + * + * Copyright JS Foundation and other contributors + * Released under the MIT license + * https://js.foundation/ + * + * Date: 2021-02-16 + */ +( function( window ) { +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + 1 * new Date(), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + nonnativeSelectorCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // Instance methods + hasOwn = ( {} ).hasOwnProperty, + arr = [], + pop = arr.pop, + pushNative = arr.push, + push = arr.push, + slice = arr.slice, + + // Use a stripped-down indexOf as it's faster than native + // https://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { + var i = 0, + len = list.length; + for ( ; i < len; i++ ) { + if ( list[ i ] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|" + + "ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + + // https://www.w3.org/TR/css-syntax-3/#ident-token-diagram + identifier = "(?:\\\\[\\da-fA-F]{1,6}" + whitespace + + "?|\\\\[^\\r\\n\\f]|[\\w-]|[^\0-\\x7f])+", + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + + // "Attribute values must be CSS identifiers [capture 5] + // or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + + whitespace + "*\\]", + + pseudos = ":(" + identifier + ")(?:\\((" + + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + + "*" ), + rdescend = new RegExp( whitespace + "|>" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + identifier + ")" ), + "CLASS": new RegExp( "^\\.(" + identifier + ")" ), + "TAG": new RegExp( "^(" + identifier + "|[*])" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + + whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + + whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace + + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rhtml = /HTML$/i, + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + + // CSS escapes + // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\[\\da-fA-F]{1,6}" + whitespace + "?|\\\\([^\\r\\n\\f])", "g" ), + funescape = function( escape, nonHex ) { + var high = "0x" + escape.slice( 1 ) - 0x10000; + + return nonHex ? + + // Strip the backslash prefix from a non-hex escape sequence + nonHex : + + // Replace a hexadecimal escape sequence with the encoded Unicode code point + // Support: IE <=11+ + // For values outside the Basic Multilingual Plane (BMP), manually construct a + // surrogate pair + high < 0 ? + String.fromCharCode( high + 0x10000 ) : + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // CSS string/identifier serialization + // https://drafts.csswg.org/cssom/#common-serializing-idioms + rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, + fcssescape = function( ch, asCodePoint ) { + if ( asCodePoint ) { + + // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER + if ( ch === "\0" ) { + return "\uFFFD"; + } + + // Control characters and (dependent upon position) numbers get escaped as code points + return ch.slice( 0, -1 ) + "\\" + + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; + } + + // Other potentially-special ASCII characters get backslash-escaped + return "\\" + ch; + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); + }, + + inDisabledFieldset = addCombinator( + function( elem ) { + return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset"; + }, + { dir: "parentNode", next: "legend" } + ); + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + ( arr = slice.call( preferredDoc.childNodes ) ), + preferredDoc.childNodes + ); + + // Support: Android<4.0 + // Detect silently failing push.apply + // eslint-disable-next-line no-unused-expressions + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + pushNative.apply( target, slice.call( els ) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + + // Can't trust NodeList.length + while ( ( target[ j++ ] = els[ i++ ] ) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var m, i, elem, nid, match, groups, newSelector, + newContext = context && context.ownerDocument, + + // nodeType defaults to 9, since context defaults to document + nodeType = context ? context.nodeType : 9; + + results = results || []; + + // Return early from calls with invalid selector or context + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + + return results; + } + + // Try to shortcut find operations (as opposed to filters) in HTML documents + if ( !seed ) { + setDocument( context ); + context = context || document; + + if ( documentIsHTML ) { + + // If the selector is sufficiently simple, try using a "get*By*" DOM method + // (excepting DocumentFragment context, where the methods don't exist) + if ( nodeType !== 11 && ( match = rquickExpr.exec( selector ) ) ) { + + // ID selector + if ( ( m = match[ 1 ] ) ) { + + // Document context + if ( nodeType === 9 ) { + if ( ( elem = context.getElementById( m ) ) ) { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + + // Element context + } else { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( newContext && ( elem = newContext.getElementById( m ) ) && + contains( context, elem ) && + elem.id === m ) { + + results.push( elem ); + return results; + } + } + + // Type selector + } else if ( match[ 2 ] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Class selector + } else if ( ( m = match[ 3 ] ) && support.getElementsByClassName && + context.getElementsByClassName ) { + + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // Take advantage of querySelectorAll + if ( support.qsa && + !nonnativeSelectorCache[ selector + " " ] && + ( !rbuggyQSA || !rbuggyQSA.test( selector ) ) && + + // Support: IE 8 only + // Exclude object elements + ( nodeType !== 1 || context.nodeName.toLowerCase() !== "object" ) ) { + + newSelector = selector; + newContext = context; + + // qSA considers elements outside a scoping root when evaluating child or + // descendant combinators, which is not what we want. + // In such cases, we work around the behavior by prefixing every selector in the + // list with an ID selector referencing the scope context. + // The technique has to be used as well when a leading combinator is used + // as such selectors are not recognized by querySelectorAll. + // Thanks to Andrew Dupont for this technique. + if ( nodeType === 1 && + ( rdescend.test( selector ) || rcombinators.test( selector ) ) ) { + + // Expand context for sibling selectors + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || + context; + + // We can use :scope instead of the ID hack if the browser + // supports it & if we're not changing the context. + if ( newContext !== context || !support.scope ) { + + // Capture the context ID, setting it first if necessary + if ( ( nid = context.getAttribute( "id" ) ) ) { + nid = nid.replace( rcssescape, fcssescape ); + } else { + context.setAttribute( "id", ( nid = expando ) ); + } + } + + // Prefix every selector in the list + groups = tokenize( selector ); + i = groups.length; + while ( i-- ) { + groups[ i ] = ( nid ? "#" + nid : ":scope" ) + " " + + toSelector( groups[ i ] ); + } + newSelector = groups.join( "," ); + } + + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch ( qsaError ) { + nonnativeSelectorCache( selector, true ); + } finally { + if ( nid === expando ) { + context.removeAttribute( "id" ); + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {function(string, object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return ( cache[ key + " " ] = value ); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created element and returns a boolean result + */ +function assert( fn ) { + var el = document.createElement( "fieldset" ); + + try { + return !!fn( el ); + } catch ( e ) { + return false; + } finally { + + // Remove from its parent by default + if ( el.parentNode ) { + el.parentNode.removeChild( el ); + } + + // release memory in IE + el = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split( "|" ), + i = arr.length; + + while ( i-- ) { + Expr.attrHandle[ arr[ i ] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + a.sourceIndex - b.sourceIndex; + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( ( cur = cur.nextSibling ) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return ( name === "input" || name === "button" ) && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for :enabled/:disabled + * @param {Boolean} disabled true for :disabled; false for :enabled + */ +function createDisabledPseudo( disabled ) { + + // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable + return function( elem ) { + + // Only certain elements can match :enabled or :disabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled + if ( "form" in elem ) { + + // Check for inherited disabledness on relevant non-disabled elements: + // * listed form-associated elements in a disabled fieldset + // https://html.spec.whatwg.org/multipage/forms.html#category-listed + // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled + // * option elements in a disabled optgroup + // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled + // All such elements have a "form" property. + if ( elem.parentNode && elem.disabled === false ) { + + // Option elements defer to a parent optgroup if present + if ( "label" in elem ) { + if ( "label" in elem.parentNode ) { + return elem.parentNode.disabled === disabled; + } else { + return elem.disabled === disabled; + } + } + + // Support: IE 6 - 11 + // Use the isDisabled shortcut property to check for disabled fieldset ancestors + return elem.isDisabled === disabled || + + // Where there is no isDisabled, check manually + /* jshint -W018 */ + elem.isDisabled !== !disabled && + inDisabledFieldset( elem ) === disabled; + } + + return elem.disabled === disabled; + + // Try to winnow out elements that can't be disabled before trusting the disabled property. + // Some victims get caught in our net (label, legend, menu, track), but it shouldn't + // even exist on them, let alone have a boolean value. + } else if ( "label" in elem ) { + return elem.disabled === disabled; + } + + // Remaining elements are neither :enabled nor :disabled + return false; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction( function( argument ) { + argument = +argument; + return markFunction( function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ ( j = matchIndexes[ i ] ) ] ) { + seed[ j ] = !( matches[ j ] = seed[ j ] ); + } + } + } ); + } ); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== "undefined" && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + var namespace = elem && elem.namespaceURI, + docElem = elem && ( elem.ownerDocument || elem ).documentElement; + + // Support: IE <=8 + // Assume HTML when documentElement doesn't yet exist, such as inside loading iframes + // https://bugs.jquery.com/ticket/4833 + return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" ); +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, subWindow, + doc = node ? node.ownerDocument || node : preferredDoc; + + // Return early if doc is invalid or already selected + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( doc == document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Update global variables + document = doc; + docElem = document.documentElement; + documentIsHTML = !isXML( document ); + + // Support: IE 9 - 11+, Edge 12 - 18+ + // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( preferredDoc != document && + ( subWindow = document.defaultView ) && subWindow.top !== subWindow ) { + + // Support: IE 11, Edge + if ( subWindow.addEventListener ) { + subWindow.addEventListener( "unload", unloadHandler, false ); + + // Support: IE 9 - 10 only + } else if ( subWindow.attachEvent ) { + subWindow.attachEvent( "onunload", unloadHandler ); + } + } + + // Support: IE 8 - 11+, Edge 12 - 18+, Chrome <=16 - 25 only, Firefox <=3.6 - 31 only, + // Safari 4 - 5 only, Opera <=11.6 - 12.x only + // IE/Edge & older browsers don't support the :scope pseudo-class. + // Support: Safari 6.0 only + // Safari 6.0 supports :scope but it's an alias of :root there. + support.scope = assert( function( el ) { + docElem.appendChild( el ).appendChild( document.createElement( "div" ) ); + return typeof el.querySelectorAll !== "undefined" && + !el.querySelectorAll( ":scope fieldset div" ).length; + } ); + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) + support.attributes = assert( function( el ) { + el.className = "i"; + return !el.getAttribute( "className" ); + } ); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert( function( el ) { + el.appendChild( document.createComment( "" ) ); + return !el.getElementsByTagName( "*" ).length; + } ); + + // Support: IE<9 + support.getElementsByClassName = rnative.test( document.getElementsByClassName ); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programmatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert( function( el ) { + docElem.appendChild( el ).id = expando; + return !document.getElementsByName || !document.getElementsByName( expando ).length; + } ); + + // ID filter and find + if ( support.getById ) { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute( "id" ) === attrId; + }; + }; + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var elem = context.getElementById( id ); + return elem ? [ elem ] : []; + } + }; + } else { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== "undefined" && + elem.getAttributeNode( "id" ); + return node && node.value === attrId; + }; + }; + + // Support: IE 6 - 7 only + // getElementById is not reliable as a find shortcut + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var node, i, elems, + elem = context.getElementById( id ); + + if ( elem ) { + + // Verify the id attribute + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + + // Fall back on getElementsByName + elems = context.getElementsByName( id ); + i = 0; + while ( ( elem = elems[ i++ ] ) ) { + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + } + } + + return []; + } + }; + } + + // Tag + Expr.find[ "TAG" ] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { + return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); + } + } : + + function( tag, context ) { + var elem, + tmp = [], + i = 0, + + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find[ "CLASS" ] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See https://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( ( support.qsa = rnative.test( document.querySelectorAll ) ) ) { + + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert( function( el ) { + + var input; + + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // https://bugs.jquery.com/ticket/12359 + docElem.appendChild( el ).innerHTML = "" + + ""; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( el.querySelectorAll( "[msallowcapture^='']" ).length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !el.querySelectorAll( "[selected]" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ + if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push( "~=" ); + } + + // Support: IE 11+, Edge 15 - 18+ + // IE 11/Edge don't find elements on a `[name='']` query in some cases. + // Adding a temporary attribute to the document before the selection works + // around the issue. + // Interestingly, IE 10 & older don't seem to have the issue. + input = document.createElement( "input" ); + input.setAttribute( "name", "" ); + el.appendChild( input ); + if ( !el.querySelectorAll( "[name='']" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*name" + whitespace + "*=" + + whitespace + "*(?:''|\"\")" ); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !el.querySelectorAll( ":checked" ).length ) { + rbuggyQSA.push( ":checked" ); + } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibling-combinator selector` fails + if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push( ".#.+[+~]" ); + } + + // Support: Firefox <=3.6 - 5 only + // Old Firefox doesn't throw on a badly-escaped identifier. + el.querySelectorAll( "\\\f" ); + rbuggyQSA.push( "[\\r\\n\\f]" ); + } ); + + assert( function( el ) { + el.innerHTML = "" + + ""; + + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = document.createElement( "input" ); + input.setAttribute( "type", "hidden" ); + el.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( el.querySelectorAll( "[name=d]" ).length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( el.querySelectorAll( ":enabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: IE9-11+ + // IE's :disabled selector does not pick up the children of disabled fieldsets + docElem.appendChild( el ).disabled = true; + if ( el.querySelectorAll( ":disabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: Opera 10 - 11 only + // Opera 10-11 does not throw on post-comma invalid pseudos + el.querySelectorAll( "*,:x" ); + rbuggyQSA.push( ",.*:" ); + } ); + } + + if ( ( support.matchesSelector = rnative.test( ( matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector ) ) ) ) { + + assert( function( el ) { + + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( el, "*" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( el, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + } ); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join( "|" ) ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join( "|" ) ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully self-exclusive + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + ) ); + } : + function( a, b ) { + if ( b ) { + while ( ( b = b.parentNode ) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + compare = ( a.ownerDocument || a ) == ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + ( !support.sortDetached && b.compareDocumentPosition( a ) === compare ) ) { + + // Choose the first element that is related to our preferred document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( a == document || a.ownerDocument == preferredDoc && + contains( preferredDoc, a ) ) { + return -1; + } + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( b == document || b.ownerDocument == preferredDoc && + contains( preferredDoc, b ) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + return a == document ? -1 : + b == document ? 1 : + /* eslint-enable eqeqeq */ + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( ( cur = cur.parentNode ) ) { + ap.unshift( cur ); + } + cur = b; + while ( ( cur = cur.parentNode ) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[ i ] === bp[ i ] ) { + i++; + } + + return i ? + + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[ i ], bp[ i ] ) : + + // Otherwise nodes in our document sort first + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + ap[ i ] == preferredDoc ? -1 : + bp[ i ] == preferredDoc ? 1 : + /* eslint-enable eqeqeq */ + 0; + }; + + return document; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + setDocument( elem ); + + if ( support.matchesSelector && documentIsHTML && + !nonnativeSelectorCache[ expr + " " ] && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch ( e ) { + nonnativeSelectorCache( expr, true ); + } + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( context.ownerDocument || context ) != document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( elem.ownerDocument || elem ) != document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; +}; + +Sizzle.escape = function( sel ) { + return ( sel + "" ).replace( rcssescape, fcssescape ); +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + + // If no nodeType, this is expected to be an array + while ( ( node = elem[ i++ ] ) ) { + + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[ 1 ] = match[ 1 ].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[ 3 ] = ( match[ 3 ] || match[ 4 ] || + match[ 5 ] || "" ).replace( runescape, funescape ); + + if ( match[ 2 ] === "~=" ) { + match[ 3 ] = " " + match[ 3 ] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[ 1 ] = match[ 1 ].toLowerCase(); + + if ( match[ 1 ].slice( 0, 3 ) === "nth" ) { + + // nth-* requires argument + if ( !match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[ 4 ] = +( match[ 4 ] ? + match[ 5 ] + ( match[ 6 ] || 1 ) : + 2 * ( match[ 3 ] === "even" || match[ 3 ] === "odd" ) ); + match[ 5 ] = +( ( match[ 7 ] + match[ 8 ] ) || match[ 3 ] === "odd" ); + + // other types prohibit arguments + } else if ( match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[ 6 ] && match[ 2 ]; + + if ( matchExpr[ "CHILD" ].test( match[ 0 ] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[ 3 ] ) { + match[ 2 ] = match[ 4 ] || match[ 5 ] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + + // Get excess from tokenize (recursively) + ( excess = tokenize( unquoted, true ) ) && + + // advance to the next closing parenthesis + ( excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length ) ) { + + // excess is a negative index + match[ 0 ] = match[ 0 ].slice( 0, excess ); + match[ 2 ] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { + return true; + } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + ( pattern = new RegExp( "(^|" + whitespace + + ")" + className + "(" + whitespace + "|$)" ) ) && classCache( + className, function( elem ) { + return pattern.test( + typeof elem.className === "string" && elem.className || + typeof elem.getAttribute !== "undefined" && + elem.getAttribute( "class" ) || + "" + ); + } ); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + /* eslint-disable max-len */ + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + /* eslint-enable max-len */ + + }; + }, + + "CHILD": function( type, what, _argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, _context, xml ) { + var cache, uniqueCache, outerCache, node, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType, + diff = false; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( ( node = node[ dir ] ) ) { + if ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) { + + return false; + } + } + + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + + // Seek `elem` from a previously-cached index + + // ...in a gzip-friendly way + node = parent; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex && cache[ 2 ]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( ( node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + } else { + + // Use previously-cached element index if available + if ( useCache ) { + + // ...in a gzip-friendly way + node = elem; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex; + } + + // xml :nth-child(...) + // or :nth-last-child(...) or :nth(-last)?-of-type(...) + if ( diff === false ) { + + // Use the same loop as above to seek `elem` from the start + while ( ( node = ++nodeIndex && node && node[ dir ] || + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + if ( ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) && + ++diff ) { + + // Cache the index of each encountered element + if ( useCache ) { + outerCache = node[ expando ] || + ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + uniqueCache[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction( function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf( seed, matched[ i ] ); + seed[ idx ] = !( matches[ idx ] = matched[ i ] ); + } + } ) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + + // Potentially complex pseudos + "not": markFunction( function( selector ) { + + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction( function( seed, matches, _context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( ( elem = unmatched[ i ] ) ) { + seed[ i ] = !( matches[ i ] = elem ); + } + } + } ) : + function( elem, _context, xml ) { + input[ 0 ] = elem; + matcher( input, null, xml, results ); + + // Don't keep the element (issue #299) + input[ 0 ] = null; + return !results.pop(); + }; + } ), + + "has": markFunction( function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + } ), + + "contains": markFunction( function( text ) { + text = text.replace( runescape, funescape ); + return function( elem ) { + return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1; + }; + } ), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + + // lang value must be a valid identifier + if ( !ridentifier.test( lang || "" ) ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( ( elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute( "xml:lang" ) || elem.getAttribute( "lang" ) ) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( ( elem = elem.parentNode ) && elem.nodeType === 1 ); + return false; + }; + } ), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && + ( !document.hasFocus || document.hasFocus() ) && + !!( elem.type || elem.href || ~elem.tabIndex ); + }, + + // Boolean properties + "enabled": createDisabledPseudo( false ), + "disabled": createDisabledPseudo( true ), + + "checked": function( elem ) { + + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return ( nodeName === "input" && !!elem.checked ) || + ( nodeName === "option" && !!elem.selected ); + }, + + "selected": function( elem ) { + + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + // eslint-disable-next-line no-unused-expressions + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos[ "empty" ]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( ( attr = elem.getAttribute( "type" ) ) == null || + attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo( function() { + return [ 0 ]; + } ), + + "last": createPositionalPseudo( function( _matchIndexes, length ) { + return [ length - 1 ]; + } ), + + "eq": createPositionalPseudo( function( _matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + } ), + + "even": createPositionalPseudo( function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "odd": createPositionalPseudo( function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "lt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? + argument + length : + argument > length ? + length : + argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "gt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ) + } +}; + +Expr.pseudos[ "nth" ] = Expr.pseudos[ "eq" ]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || ( match = rcomma.exec( soFar ) ) ) { + if ( match ) { + + // Don't consume trailing commas as valid + soFar = soFar.slice( match[ 0 ].length ) || soFar; + } + groups.push( ( tokens = [] ) ); + } + + matched = false; + + // Combinators + if ( ( match = rcombinators.exec( soFar ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + + // Cast descendant combinators to space + type: match[ 0 ].replace( rtrim, " " ) + } ); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( ( match = matchExpr[ type ].exec( soFar ) ) && ( !preFilters[ type ] || + ( match = preFilters[ type ]( match ) ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + type: type, + matches: match + } ); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[ i ].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + skip = combinator.next, + key = skip || dir, + checkNonElements = base && key === "parentNode", + doneName = done++; + + return combinator.first ? + + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + return false; + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, uniqueCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching + if ( xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || ( elem[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ elem.uniqueID ] || + ( outerCache[ elem.uniqueID ] = {} ); + + if ( skip && skip === elem.nodeName.toLowerCase() ) { + elem = elem[ dir ] || elem; + } else if ( ( oldCache = uniqueCache[ key ] ) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return ( newCache[ 2 ] = oldCache[ 2 ] ); + } else { + + // Reuse newcache so results back-propagate to previous elements + uniqueCache[ key ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( ( newCache[ 2 ] = matcher( elem, context, xml ) ) ) { + return true; + } + } + } + } + } + return false; + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[ i ]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[ 0 ]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[ i ], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( ( elem = unmatched[ i ] ) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction( function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( + selector || "*", + context.nodeType ? [ context ] : context, + [] + ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( ( elem = temp[ i ] ) ) { + matcherOut[ postMap[ i ] ] = !( matcherIn[ postMap[ i ] ] = elem ); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) ) { + + // Restore matcherIn since elem is not yet a final match + temp.push( ( matcherIn[ i ] = elem ) ); + } + } + postFinder( null, ( matcherOut = [] ), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) && + ( temp = postFinder ? indexOf( seed, elem ) : preMap[ i ] ) > -1 ) { + + seed[ temp ] = !( results[ temp ] = elem ); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + } ); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[ 0 ].type ], + implicitRelative = leadingRelative || Expr.relative[ " " ], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + ( checkContext = context ).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; + } ]; + + for ( ; i < len; i++ ) { + if ( ( matcher = Expr.relative[ tokens[ i ].type ] ) ) { + matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ]; + } else { + matcher = Expr.filter[ tokens[ i ].type ].apply( null, tokens[ i ].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[ j ].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens + .slice( 0, i - 1 ) + .concat( { value: tokens[ i - 2 ].type === " " ? "*" : "" } ) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( ( tokens = tokens.slice( j ) ) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find[ "TAG" ]( "*", outermost ), + + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = ( dirruns += contextBackup == null ? 1 : Math.random() || 0.1 ), + len = elems.length; + + if ( outermost ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + outermostContext = context == document || context || outermost; + } + + // Add elements passing elementMatchers directly to results + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id + for ( ; i !== len && ( elem = elems[ i ] ) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( !context && elem.ownerDocument != document ) { + setDocument( elem ); + xml = !documentIsHTML; + } + while ( ( matcher = elementMatchers[ j++ ] ) ) { + if ( matcher( elem, context || document, xml ) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + + // They will have gone through all possible matchers + if ( ( elem = !matcher && elem ) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // `i` is now the count of elements visited above, and adding it to `matchedCount` + // makes the latter nonnegative. + matchedCount += i; + + // Apply set filters to unmatched elements + // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` + // equals `i`), unless we didn't visit _any_ elements in the above loop because we have + // no element matchers and no seed. + // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that + // case, which will result in a "00" `matchedCount` that differs from `i` but is also + // numerically zero. + if ( bySet && i !== matchedCount ) { + j = 0; + while ( ( matcher = setMatchers[ j++ ] ) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !( unmatched[ i ] || setMatched[ i ] ) ) { + setMatched[ i ] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[ i ] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( + selector, + matcherFromGroupMatchers( elementMatchers, setMatchers ) + ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( ( selector = compiled.selector || selector ) ); + + results = results || []; + + // Try to minimize operations if there is only one selector in the list and no seed + // (the latter of which guarantees us context) + if ( match.length === 1 ) { + + // Reduce context if the leading compound selector is an ID + tokens = match[ 0 ] = match[ 0 ].slice( 0 ); + if ( tokens.length > 2 && ( token = tokens[ 0 ] ).type === "ID" && + context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[ 1 ].type ] ) { + + context = ( Expr.find[ "ID" ]( token.matches[ 0 ] + .replace( runescape, funescape ), context ) || [] )[ 0 ]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr[ "needsContext" ].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[ i ]; + + // Abort if we hit a combinator + if ( Expr.relative[ ( type = token.type ) ] ) { + break; + } + if ( ( find = Expr.find[ type ] ) ) { + + // Search, expanding context for leading sibling combinators + if ( ( seed = find( + token.matches[ 0 ].replace( runescape, funescape ), + rsibling.test( tokens[ 0 ].type ) && testContext( context.parentNode ) || + context + ) ) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + !context || rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split( "" ).sort( sortOrder ).join( "" ) === expando; + +// Support: Chrome 14-35+ +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert( function( el ) { + + // Should return 1, but returns 4 (following) + return el.compareDocumentPosition( document.createElement( "fieldset" ) ) & 1; +} ); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert( function( el ) { + el.innerHTML = ""; + return el.firstChild.getAttribute( "href" ) === "#"; +} ) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + } ); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert( function( el ) { + el.innerHTML = ""; + el.firstChild.setAttribute( "value", "" ); + return el.firstChild.getAttribute( "value" ) === ""; +} ) ) { + addHandle( "value", function( elem, _name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + } ); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert( function( el ) { + return el.getAttribute( "disabled" ) == null; +} ) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; + } + } ); +} + +return Sizzle; + +} )( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; + +// Deprecated +jQuery.expr[ ":" ] = jQuery.expr.pseudos; +jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; +jQuery.escapeSelector = Sizzle.escape; + + + + +var dir = function( elem, dir, until ) { + var matched = [], + truncate = until !== undefined; + + while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { + if ( elem.nodeType === 1 ) { + if ( truncate && jQuery( elem ).is( until ) ) { + break; + } + matched.push( elem ); + } + } + return matched; +}; + + +var siblings = function( n, elem ) { + var matched = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + matched.push( n ); + } + } + + return matched; +}; + + +var rneedsContext = jQuery.expr.match.needsContext; + + + +function nodeName( elem, name ) { + + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + +} +var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); + + + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + return !!qualifier.call( elem, i, elem ) !== not; + } ); + } + + // Single element + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + } ); + } + + // Arraylike of elements (jQuery, arguments, Array) + if ( typeof qualifier !== "string" ) { + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not; + } ); + } + + // Filtered directly for both simple and complex selectors + return jQuery.filter( qualifier, elements, not ); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + if ( elems.length === 1 && elem.nodeType === 1 ) { + return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; + } + + return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + } ) ); +}; + +jQuery.fn.extend( { + find: function( selector ) { + var i, ret, + len = this.length, + self = this; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter( function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + } ) ); + } + + ret = this.pushStack( [] ); + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + return len > 1 ? jQuery.uniqueSort( ret ) : ret; + }, + filter: function( selector ) { + return this.pushStack( winnow( this, selector || [], false ) ); + }, + not: function( selector ) { + return this.pushStack( winnow( this, selector || [], true ) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +} ); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // A simple way to check for HTML strings + // Prioritize #id over to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + // Shortcut simple #id case for speed + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, + + init = jQuery.fn.init = function( selector, context, root ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Method init() accepts an alternate rootjQuery + // so migrate can support jQuery.sub (gh-2101) + root = root || rootjQuery; + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector[ 0 ] === "<" && + selector[ selector.length - 1 ] === ">" && + selector.length >= 3 ) { + + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && ( match[ 1 ] || !context ) ) { + + // HANDLE: $(html) -> $(array) + if ( match[ 1 ] ) { + context = context instanceof jQuery ? context[ 0 ] : context; + + // Option to run scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[ 1 ], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + + // Properties of context are called as methods if possible + if ( isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[ 2 ] ); + + if ( elem ) { + + // Inject the element directly into the jQuery object + this[ 0 ] = elem; + this.length = 1; + } + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || root ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this[ 0 ] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( isFunction( selector ) ) { + return root.ready !== undefined ? + root.ready( selector ) : + + // Execute immediately if ready is not present + selector( jQuery ); + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + + // Methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.fn.extend( { + has: function( target ) { + var targets = jQuery( target, this ), + l = targets.length; + + return this.filter( function() { + var i = 0; + for ( ; i < l; i++ ) { + if ( jQuery.contains( this, targets[ i ] ) ) { + return true; + } + } + } ); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + targets = typeof selectors !== "string" && jQuery( selectors ); + + // Positional selectors never match, since there's no _selection_ context + if ( !rneedsContext.test( selectors ) ) { + for ( ; i < l; i++ ) { + for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { + + // Always skip document fragments + if ( cur.nodeType < 11 && ( targets ? + targets.index( cur ) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector( cur, selectors ) ) ) { + + matched.push( cur ); + break; + } + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); + }, + + // Determine the position of an element within the set + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; + } + + // Index in selector + if ( typeof elem === "string" ) { + return indexOf.call( jQuery( elem ), this[ 0 ] ); + } + + // Locate the position of the desired element + return indexOf.call( this, + + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[ 0 ] : elem + ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.uniqueSort( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter( selector ) + ); + } +} ); + +function sibling( cur, dir ) { + while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} + return cur; +} + +jQuery.each( { + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, _i, until ) { + return dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, _i, until ) { + return dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, _i, until ) { + return dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return siblings( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return siblings( elem.firstChild ); + }, + contents: function( elem ) { + if ( elem.contentDocument != null && + + // Support: IE 11+ + // elements with no `data` attribute has an object + // `contentDocument` with a `null` prototype. + getProto( elem.contentDocument ) ) { + + return elem.contentDocument; + } + + // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only + // Treat the template element as a regular one in browsers that + // don't support it. + if ( nodeName( elem, "template" ) ) { + elem = elem.content || elem; + } + + return jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var matched = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + matched = jQuery.filter( selector, matched ); + } + + if ( this.length > 1 ) { + + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + jQuery.uniqueSort( matched ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + matched.reverse(); + } + } + + return this.pushStack( matched ); + }; +} ); +var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); + + + +// Convert String-formatted options into Object-formatted ones +function createOptions( options ) { + var object = {}; + jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { + object[ flag ] = true; + } ); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + createOptions( options ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + + // Last fire value for non-forgettable lists + memory, + + // Flag to know if list was already fired + fired, + + // Flag to prevent firing + locked, + + // Actual callback list + list = [], + + // Queue of execution data for repeatable lists + queue = [], + + // Index of currently firing callback (modified by add/remove as needed) + firingIndex = -1, + + // Fire callbacks + fire = function() { + + // Enforce single-firing + locked = locked || options.once; + + // Execute callbacks for all pending executions, + // respecting firingIndex overrides and runtime changes + fired = firing = true; + for ( ; queue.length; firingIndex = -1 ) { + memory = queue.shift(); + while ( ++firingIndex < list.length ) { + + // Run callback and check for early termination + if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && + options.stopOnFalse ) { + + // Jump to end and forget the data so .add doesn't re-fire + firingIndex = list.length; + memory = false; + } + } + } + + // Forget the data if we're done with it + if ( !options.memory ) { + memory = false; + } + + firing = false; + + // Clean up if we're done firing for good + if ( locked ) { + + // Keep an empty list if we have data for future add calls + if ( memory ) { + list = []; + + // Otherwise, this object is spent + } else { + list = ""; + } + } + }, + + // Actual Callbacks object + self = { + + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + + // If we have memory from a past run, we should fire after adding + if ( memory && !firing ) { + firingIndex = list.length - 1; + queue.push( memory ); + } + + ( function add( args ) { + jQuery.each( args, function( _, arg ) { + if ( isFunction( arg ) ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && toType( arg ) !== "string" ) { + + // Inspect recursively + add( arg ); + } + } ); + } )( arguments ); + + if ( memory && !firing ) { + fire(); + } + } + return this; + }, + + // Remove a callback from the list + remove: function() { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + + // Handle firing indexes + if ( index <= firingIndex ) { + firingIndex--; + } + } + } ); + return this; + }, + + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? + jQuery.inArray( fn, list ) > -1 : + list.length > 0; + }, + + // Remove all callbacks from the list + empty: function() { + if ( list ) { + list = []; + } + return this; + }, + + // Disable .fire and .add + // Abort any current/pending executions + // Clear all callbacks and values + disable: function() { + locked = queue = []; + list = memory = ""; + return this; + }, + disabled: function() { + return !list; + }, + + // Disable .fire + // Also disable .add unless we have memory (since it would have no effect) + // Abort any pending executions + lock: function() { + locked = queue = []; + if ( !memory && !firing ) { + list = memory = ""; + } + return this; + }, + locked: function() { + return !!locked; + }, + + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( !locked ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + queue.push( args ); + if ( !firing ) { + fire(); + } + } + return this; + }, + + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +function Identity( v ) { + return v; +} +function Thrower( ex ) { + throw ex; +} + +function adoptValue( value, resolve, reject, noValue ) { + var method; + + try { + + // Check for promise aspect first to privilege synchronous behavior + if ( value && isFunction( ( method = value.promise ) ) ) { + method.call( value ).done( resolve ).fail( reject ); + + // Other thenables + } else if ( value && isFunction( ( method = value.then ) ) ) { + method.call( value, resolve, reject ); + + // Other non-thenables + } else { + + // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: + // * false: [ value ].slice( 0 ) => resolve( value ) + // * true: [ value ].slice( 1 ) => resolve() + resolve.apply( undefined, [ value ].slice( noValue ) ); + } + + // For Promises/A+, convert exceptions into rejections + // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in + // Deferred#then to conditionally suppress rejection. + } catch ( value ) { + + // Support: Android 4.0 only + // Strict mode functions invoked without .call/.apply get global-object context + reject.apply( undefined, [ value ] ); + } +} + +jQuery.extend( { + + Deferred: function( func ) { + var tuples = [ + + // action, add listener, callbacks, + // ... .then handlers, argument index, [final state] + [ "notify", "progress", jQuery.Callbacks( "memory" ), + jQuery.Callbacks( "memory" ), 2 ], + [ "resolve", "done", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 0, "resolved" ], + [ "reject", "fail", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 1, "rejected" ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + "catch": function( fn ) { + return promise.then( null, fn ); + }, + + // Keep pipe for back-compat + pipe: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + + return jQuery.Deferred( function( newDefer ) { + jQuery.each( tuples, function( _i, tuple ) { + + // Map tuples (progress, done, fail) to arguments (done, fail, progress) + var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; + + // deferred.progress(function() { bind to newDefer or newDefer.notify }) + // deferred.done(function() { bind to newDefer or newDefer.resolve }) + // deferred.fail(function() { bind to newDefer or newDefer.reject }) + deferred[ tuple[ 1 ] ]( function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && isFunction( returned.promise ) ) { + returned.promise() + .progress( newDefer.notify ) + .done( newDefer.resolve ) + .fail( newDefer.reject ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( + this, + fn ? [ returned ] : arguments + ); + } + } ); + } ); + fns = null; + } ).promise(); + }, + then: function( onFulfilled, onRejected, onProgress ) { + var maxDepth = 0; + function resolve( depth, deferred, handler, special ) { + return function() { + var that = this, + args = arguments, + mightThrow = function() { + var returned, then; + + // Support: Promises/A+ section 2.3.3.3.3 + // https://promisesaplus.com/#point-59 + // Ignore double-resolution attempts + if ( depth < maxDepth ) { + return; + } + + returned = handler.apply( that, args ); + + // Support: Promises/A+ section 2.3.1 + // https://promisesaplus.com/#point-48 + if ( returned === deferred.promise() ) { + throw new TypeError( "Thenable self-resolution" ); + } + + // Support: Promises/A+ sections 2.3.3.1, 3.5 + // https://promisesaplus.com/#point-54 + // https://promisesaplus.com/#point-75 + // Retrieve `then` only once + then = returned && + + // Support: Promises/A+ section 2.3.4 + // https://promisesaplus.com/#point-64 + // Only check objects and functions for thenability + ( typeof returned === "object" || + typeof returned === "function" ) && + returned.then; + + // Handle a returned thenable + if ( isFunction( then ) ) { + + // Special processors (notify) just wait for resolution + if ( special ) { + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ) + ); + + // Normal processors (resolve) also hook into progress + } else { + + // ...and disregard older resolution values + maxDepth++; + + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ), + resolve( maxDepth, deferred, Identity, + deferred.notifyWith ) + ); + } + + // Handle all other returned values + } else { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Identity ) { + that = undefined; + args = [ returned ]; + } + + // Process the value(s) + // Default process is resolve + ( special || deferred.resolveWith )( that, args ); + } + }, + + // Only normal processors (resolve) catch and reject exceptions + process = special ? + mightThrow : + function() { + try { + mightThrow(); + } catch ( e ) { + + if ( jQuery.Deferred.exceptionHook ) { + jQuery.Deferred.exceptionHook( e, + process.stackTrace ); + } + + // Support: Promises/A+ section 2.3.3.3.4.1 + // https://promisesaplus.com/#point-61 + // Ignore post-resolution exceptions + if ( depth + 1 >= maxDepth ) { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Thrower ) { + that = undefined; + args = [ e ]; + } + + deferred.rejectWith( that, args ); + } + } + }; + + // Support: Promises/A+ section 2.3.3.3.1 + // https://promisesaplus.com/#point-57 + // Re-resolve promises immediately to dodge false rejection from + // subsequent errors + if ( depth ) { + process(); + } else { + + // Call an optional hook to record the stack, in case of exception + // since it's otherwise lost when execution goes async + if ( jQuery.Deferred.getStackHook ) { + process.stackTrace = jQuery.Deferred.getStackHook(); + } + window.setTimeout( process ); + } + }; + } + + return jQuery.Deferred( function( newDefer ) { + + // progress_handlers.add( ... ) + tuples[ 0 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onProgress ) ? + onProgress : + Identity, + newDefer.notifyWith + ) + ); + + // fulfilled_handlers.add( ... ) + tuples[ 1 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onFulfilled ) ? + onFulfilled : + Identity + ) + ); + + // rejected_handlers.add( ... ) + tuples[ 2 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onRejected ) ? + onRejected : + Thrower + ) + ); + } ).promise(); + }, + + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 5 ]; + + // promise.progress = list.add + // promise.done = list.add + // promise.fail = list.add + promise[ tuple[ 1 ] ] = list.add; + + // Handle state + if ( stateString ) { + list.add( + function() { + + // state = "resolved" (i.e., fulfilled) + // state = "rejected" + state = stateString; + }, + + // rejected_callbacks.disable + // fulfilled_callbacks.disable + tuples[ 3 - i ][ 2 ].disable, + + // rejected_handlers.disable + // fulfilled_handlers.disable + tuples[ 3 - i ][ 3 ].disable, + + // progress_callbacks.lock + tuples[ 0 ][ 2 ].lock, + + // progress_handlers.lock + tuples[ 0 ][ 3 ].lock + ); + } + + // progress_handlers.fire + // fulfilled_handlers.fire + // rejected_handlers.fire + list.add( tuple[ 3 ].fire ); + + // deferred.notify = function() { deferred.notifyWith(...) } + // deferred.resolve = function() { deferred.resolveWith(...) } + // deferred.reject = function() { deferred.rejectWith(...) } + deferred[ tuple[ 0 ] ] = function() { + deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); + return this; + }; + + // deferred.notifyWith = list.fireWith + // deferred.resolveWith = list.fireWith + // deferred.rejectWith = list.fireWith + deferred[ tuple[ 0 ] + "With" ] = list.fireWith; + } ); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( singleValue ) { + var + + // count of uncompleted subordinates + remaining = arguments.length, + + // count of unprocessed arguments + i = remaining, + + // subordinate fulfillment data + resolveContexts = Array( i ), + resolveValues = slice.call( arguments ), + + // the primary Deferred + primary = jQuery.Deferred(), + + // subordinate callback factory + updateFunc = function( i ) { + return function( value ) { + resolveContexts[ i ] = this; + resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( !( --remaining ) ) { + primary.resolveWith( resolveContexts, resolveValues ); + } + }; + }; + + // Single- and empty arguments are adopted like Promise.resolve + if ( remaining <= 1 ) { + adoptValue( singleValue, primary.done( updateFunc( i ) ).resolve, primary.reject, + !remaining ); + + // Use .then() to unwrap secondary thenables (cf. gh-3000) + if ( primary.state() === "pending" || + isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { + + return primary.then(); + } + } + + // Multiple arguments are aggregated like Promise.all array elements + while ( i-- ) { + adoptValue( resolveValues[ i ], updateFunc( i ), primary.reject ); + } + + return primary.promise(); + } +} ); + + +// These usually indicate a programmer mistake during development, +// warn about them ASAP rather than swallowing them by default. +var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; + +jQuery.Deferred.exceptionHook = function( error, stack ) { + + // Support: IE 8 - 9 only + // Console exists when dev tools are open, which can happen at any time + if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { + window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); + } +}; + + + + +jQuery.readyException = function( error ) { + window.setTimeout( function() { + throw error; + } ); +}; + + + + +// The deferred used on DOM ready +var readyList = jQuery.Deferred(); + +jQuery.fn.ready = function( fn ) { + + readyList + .then( fn ) + + // Wrap jQuery.readyException in a function so that the lookup + // happens at the time of error handling instead of callback + // registration. + .catch( function( error ) { + jQuery.readyException( error ); + } ); + + return this; +}; + +jQuery.extend( { + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + } +} ); + +jQuery.ready.then = readyList.then; + +// The ready event handler and self cleanup method +function completed() { + document.removeEventListener( "DOMContentLoaded", completed ); + window.removeEventListener( "load", completed ); + jQuery.ready(); +} + +// Catch cases where $(document).ready() is called +// after the browser event has already occurred. +// Support: IE <=9 - 10 only +// Older IE sometimes signals "interactive" too soon +if ( document.readyState === "complete" || + ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { + + // Handle it asynchronously to allow scripts the opportunity to delay ready + window.setTimeout( jQuery.ready ); + +} else { + + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed ); +} + + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + len = elems.length, + bulk = key == null; + + // Sets many values + if ( toType( key ) === "object" ) { + chainable = true; + for ( i in key ) { + access( elems, fn, i, key[ i ], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, _key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < len; i++ ) { + fn( + elems[ i ], key, raw ? + value : + value.call( elems[ i ], i, fn( elems[ i ], key ) ) + ); + } + } + } + + if ( chainable ) { + return elems; + } + + // Gets + if ( bulk ) { + return fn.call( elems ); + } + + return len ? fn( elems[ 0 ], key ) : emptyGet; +}; + + +// Matches dashed string for camelizing +var rmsPrefix = /^-ms-/, + rdashAlpha = /-([a-z])/g; + +// Used by camelCase as callback to replace() +function fcamelCase( _all, letter ) { + return letter.toUpperCase(); +} + +// Convert dashed to camelCase; used by the css and data modules +// Support: IE <=9 - 11, Edge 12 - 15 +// Microsoft forgot to hump their vendor prefix (#9572) +function camelCase( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); +} +var acceptData = function( owner ) { + + // Accepts only: + // - Node + // - Node.ELEMENT_NODE + // - Node.DOCUMENT_NODE + // - Object + // - Any + return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); +}; + + + + +function Data() { + this.expando = jQuery.expando + Data.uid++; +} + +Data.uid = 1; + +Data.prototype = { + + cache: function( owner ) { + + // Check if the owner object already has a cache + var value = owner[ this.expando ]; + + // If not, create one + if ( !value ) { + value = {}; + + // We can accept data for non-element nodes in modern browsers, + // but we should not, see #8335. + // Always return an empty object. + if ( acceptData( owner ) ) { + + // If it is a node unlikely to be stringify-ed or looped over + // use plain assignment + if ( owner.nodeType ) { + owner[ this.expando ] = value; + + // Otherwise secure it in a non-enumerable property + // configurable must be true to allow the property to be + // deleted when data is removed + } else { + Object.defineProperty( owner, this.expando, { + value: value, + configurable: true + } ); + } + } + } + + return value; + }, + set: function( owner, data, value ) { + var prop, + cache = this.cache( owner ); + + // Handle: [ owner, key, value ] args + // Always use camelCase key (gh-2257) + if ( typeof data === "string" ) { + cache[ camelCase( data ) ] = value; + + // Handle: [ owner, { properties } ] args + } else { + + // Copy the properties one-by-one to the cache object + for ( prop in data ) { + cache[ camelCase( prop ) ] = data[ prop ]; + } + } + return cache; + }, + get: function( owner, key ) { + return key === undefined ? + this.cache( owner ) : + + // Always use camelCase key (gh-2257) + owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ]; + }, + access: function( owner, key, value ) { + + // In cases where either: + // + // 1. No key was specified + // 2. A string key was specified, but no value provided + // + // Take the "read" path and allow the get method to determine + // which value to return, respectively either: + // + // 1. The entire cache object + // 2. The data stored at the key + // + if ( key === undefined || + ( ( key && typeof key === "string" ) && value === undefined ) ) { + + return this.get( owner, key ); + } + + // When the key is not a string, or both a key and value + // are specified, set or extend (existing objects) with either: + // + // 1. An object of properties + // 2. A key and value + // + this.set( owner, key, value ); + + // Since the "set" path can have two possible entry points + // return the expected data based on which path was taken[*] + return value !== undefined ? value : key; + }, + remove: function( owner, key ) { + var i, + cache = owner[ this.expando ]; + + if ( cache === undefined ) { + return; + } + + if ( key !== undefined ) { + + // Support array or space separated string of keys + if ( Array.isArray( key ) ) { + + // If key is an array of keys... + // We always set camelCase keys, so remove that. + key = key.map( camelCase ); + } else { + key = camelCase( key ); + + // If a key with the spaces exists, use it. + // Otherwise, create an array by matching non-whitespace + key = key in cache ? + [ key ] : + ( key.match( rnothtmlwhite ) || [] ); + } + + i = key.length; + + while ( i-- ) { + delete cache[ key[ i ] ]; + } + } + + // Remove the expando if there's no more data + if ( key === undefined || jQuery.isEmptyObject( cache ) ) { + + // Support: Chrome <=35 - 45 + // Webkit & Blink performance suffers when deleting properties + // from DOM nodes, so set to undefined instead + // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) + if ( owner.nodeType ) { + owner[ this.expando ] = undefined; + } else { + delete owner[ this.expando ]; + } + } + }, + hasData: function( owner ) { + var cache = owner[ this.expando ]; + return cache !== undefined && !jQuery.isEmptyObject( cache ); + } +}; +var dataPriv = new Data(); + +var dataUser = new Data(); + + + +// Implementation Summary +// +// 1. Enforce API surface and semantic compatibility with 1.9.x branch +// 2. Improve the module's maintainability by reducing the storage +// paths to a single mechanism. +// 3. Use the same single mechanism to support "private" and "user" data. +// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) +// 5. Avoid exposing implementation details on user objects (eg. expando properties) +// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /[A-Z]/g; + +function getData( data ) { + if ( data === "true" ) { + return true; + } + + if ( data === "false" ) { + return false; + } + + if ( data === "null" ) { + return null; + } + + // Only convert to a number if it doesn't change the string + if ( data === +data + "" ) { + return +data; + } + + if ( rbrace.test( data ) ) { + return JSON.parse( data ); + } + + return data; +} + +function dataAttr( elem, key, data ) { + var name; + + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = getData( data ); + } catch ( e ) {} + + // Make sure we set the data so it isn't changed later + dataUser.set( elem, key, data ); + } else { + data = undefined; + } + } + return data; +} + +jQuery.extend( { + hasData: function( elem ) { + return dataUser.hasData( elem ) || dataPriv.hasData( elem ); + }, + + data: function( elem, name, data ) { + return dataUser.access( elem, name, data ); + }, + + removeData: function( elem, name ) { + dataUser.remove( elem, name ); + }, + + // TODO: Now that all calls to _data and _removeData have been replaced + // with direct calls to dataPriv methods, these can be deprecated. + _data: function( elem, name, data ) { + return dataPriv.access( elem, name, data ); + }, + + _removeData: function( elem, name ) { + dataPriv.remove( elem, name ); + } +} ); + +jQuery.fn.extend( { + data: function( key, value ) { + var i, name, data, + elem = this[ 0 ], + attrs = elem && elem.attributes; + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = dataUser.get( elem ); + + if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE 11 only + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = camelCase( name.slice( 5 ) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + dataPriv.set( elem, "hasDataAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each( function() { + dataUser.set( this, key ); + } ); + } + + return access( this, function( value ) { + var data; + + // The calling jQuery object (element matches) is not empty + // (and therefore has an element appears at this[ 0 ]) and the + // `value` parameter was not undefined. An empty jQuery object + // will result in `undefined` for elem = this[ 0 ] which will + // throw an exception if an attempt to read a data cache is made. + if ( elem && value === undefined ) { + + // Attempt to get data from the cache + // The key will always be camelCased in Data + data = dataUser.get( elem, key ); + if ( data !== undefined ) { + return data; + } + + // Attempt to "discover" the data in + // HTML5 custom data-* attrs + data = dataAttr( elem, key ); + if ( data !== undefined ) { + return data; + } + + // We tried really hard, but the data doesn't exist. + return; + } + + // Set the data... + this.each( function() { + + // We always store the camelCased key + dataUser.set( this, key, value ); + } ); + }, null, value, arguments.length > 1, null, true ); + }, + + removeData: function( key ) { + return this.each( function() { + dataUser.remove( this, key ); + } ); + } +} ); + + +jQuery.extend( { + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = dataPriv.get( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || Array.isArray( data ) ) { + queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // Clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // Not public - generate a queueHooks object, or return the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { + empty: jQuery.Callbacks( "once memory" ).add( function() { + dataPriv.remove( elem, [ type + "queue", key ] ); + } ) + } ); + } +} ); + +jQuery.fn.extend( { + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[ 0 ], type ); + } + + return data === undefined ? + this : + this.each( function() { + var queue = jQuery.queue( this, type, data ); + + // Ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + } ); + }, + dequeue: function( type ) { + return this.each( function() { + jQuery.dequeue( this, type ); + } ); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +} ); +var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; + +var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); + + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var documentElement = document.documentElement; + + + + var isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ); + }, + composed = { composed: true }; + + // Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only + // Check attachment across shadow DOM boundaries when possible (gh-3504) + // Support: iOS 10.0-10.2 only + // Early iOS 10 versions support `attachShadow` but not `getRootNode`, + // leading to errors. We need to check for `getRootNode`. + if ( documentElement.getRootNode ) { + isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ) || + elem.getRootNode( composed ) === elem.ownerDocument; + }; + } +var isHiddenWithinTree = function( elem, el ) { + + // isHiddenWithinTree might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + + // Inline style trumps all + return elem.style.display === "none" || + elem.style.display === "" && + + // Otherwise, check computed style + // Support: Firefox <=43 - 45 + // Disconnected elements can have computed display: none, so first confirm that elem is + // in the document. + isAttached( elem ) && + + jQuery.css( elem, "display" ) === "none"; + }; + + + +function adjustCSS( elem, prop, valueParts, tween ) { + var adjusted, scale, + maxIterations = 20, + currentValue = tween ? + function() { + return tween.cur(); + } : + function() { + return jQuery.css( elem, prop, "" ); + }, + initial = currentValue(), + unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + initialInUnit = elem.nodeType && + ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && + rcssNum.exec( jQuery.css( elem, prop ) ); + + if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { + + // Support: Firefox <=54 + // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144) + initial = initial / 2; + + // Trust units reported by jQuery.css + unit = unit || initialInUnit[ 3 ]; + + // Iteratively approximate from a nonzero starting point + initialInUnit = +initial || 1; + + while ( maxIterations-- ) { + + // Evaluate and update our best guess (doubling guesses that zero out). + // Finish if the scale equals or crosses 1 (making the old*new product non-positive). + jQuery.style( elem, prop, initialInUnit + unit ); + if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) { + maxIterations = 0; + } + initialInUnit = initialInUnit / scale; + + } + + initialInUnit = initialInUnit * 2; + jQuery.style( elem, prop, initialInUnit + unit ); + + // Make sure we update the tween properties later on + valueParts = valueParts || []; + } + + if ( valueParts ) { + initialInUnit = +initialInUnit || +initial || 0; + + // Apply relative offset (+=/-=) if specified + adjusted = valueParts[ 1 ] ? + initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : + +valueParts[ 2 ]; + if ( tween ) { + tween.unit = unit; + tween.start = initialInUnit; + tween.end = adjusted; + } + } + return adjusted; +} + + +var defaultDisplayMap = {}; + +function getDefaultDisplay( elem ) { + var temp, + doc = elem.ownerDocument, + nodeName = elem.nodeName, + display = defaultDisplayMap[ nodeName ]; + + if ( display ) { + return display; + } + + temp = doc.body.appendChild( doc.createElement( nodeName ) ); + display = jQuery.css( temp, "display" ); + + temp.parentNode.removeChild( temp ); + + if ( display === "none" ) { + display = "block"; + } + defaultDisplayMap[ nodeName ] = display; + + return display; +} + +function showHide( elements, show ) { + var display, elem, + values = [], + index = 0, + length = elements.length; + + // Determine new display value for elements that need to change + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + display = elem.style.display; + if ( show ) { + + // Since we force visibility upon cascade-hidden elements, an immediate (and slow) + // check is required in this first loop unless we have a nonempty display value (either + // inline or about-to-be-restored) + if ( display === "none" ) { + values[ index ] = dataPriv.get( elem, "display" ) || null; + if ( !values[ index ] ) { + elem.style.display = ""; + } + } + if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { + values[ index ] = getDefaultDisplay( elem ); + } + } else { + if ( display !== "none" ) { + values[ index ] = "none"; + + // Remember what we're overwriting + dataPriv.set( elem, "display", display ); + } + } + } + + // Set the display of the elements in a second loop to avoid constant reflow + for ( index = 0; index < length; index++ ) { + if ( values[ index ] != null ) { + elements[ index ].style.display = values[ index ]; + } + } + + return elements; +} + +jQuery.fn.extend( { + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each( function() { + if ( isHiddenWithinTree( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + } ); + } +} ); +var rcheckableType = ( /^(?:checkbox|radio)$/i ); + +var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i ); + +var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i ); + + + +( function() { + var fragment = document.createDocumentFragment(), + div = fragment.appendChild( document.createElement( "div" ) ), + input = document.createElement( "input" ); + + // Support: Android 4.0 - 4.3 only + // Check state lost if the name is set (#11217) + // Support: Windows Web Apps (WWA) + // `name` and `type` must use .setAttribute for WWA (#14901) + input.setAttribute( "type", "radio" ); + input.setAttribute( "checked", "checked" ); + input.setAttribute( "name", "t" ); + + div.appendChild( input ); + + // Support: Android <=4.1 only + // Older WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE <=11 only + // Make sure textarea (and checkbox) defaultValue is properly cloned + div.innerHTML = ""; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; + + // Support: IE <=9 only + // IE <=9 replaces "; + support.option = !!div.lastChild; +} )(); + + +// We have to close these tags to support XHTML (#13200) +var wrapMap = { + + // XHTML parsers do not magically insert elements in the + // same way that tag soup parsers do. So we cannot shorten + // this by omitting or other required elements. + thead: [ 1, "", "
" ], + col: [ 2, "", "
" ], + tr: [ 2, "", "
" ], + td: [ 3, "", "
" ], + + _default: [ 0, "", "" ] +}; + +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + +// Support: IE <=9 only +if ( !support.option ) { + wrapMap.optgroup = wrapMap.option = [ 1, "" ]; +} + + +function getAll( context, tag ) { + + // Support: IE <=9 - 11 only + // Use typeof to avoid zero-argument method invocation on host objects (#15151) + var ret; + + if ( typeof context.getElementsByTagName !== "undefined" ) { + ret = context.getElementsByTagName( tag || "*" ); + + } else if ( typeof context.querySelectorAll !== "undefined" ) { + ret = context.querySelectorAll( tag || "*" ); + + } else { + ret = []; + } + + if ( tag === undefined || tag && nodeName( context, tag ) ) { + return jQuery.merge( [ context ], ret ); + } + + return ret; +} + + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + dataPriv.set( + elems[ i ], + "globalEval", + !refElements || dataPriv.get( refElements[ i ], "globalEval" ) + ); + } +} + + +var rhtml = /<|&#?\w+;/; + +function buildFragment( elems, context, scripts, selection, ignored ) { + var elem, tmp, tag, wrap, attached, j, + fragment = context.createDocumentFragment(), + nodes = [], + i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( toType( elem ) === "object" ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); + + // Deserialize a standard representation + tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; + + // Descend through wrappers to the right content + j = wrap[ 0 ]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, tmp.childNodes ); + + // Remember the top-level container + tmp = fragment.firstChild; + + // Ensure the created nodes are orphaned (#12392) + tmp.textContent = ""; + } + } + } + + // Remove wrapper from fragment + fragment.textContent = ""; + + i = 0; + while ( ( elem = nodes[ i++ ] ) ) { + + // Skip elements already in the context collection (trac-4087) + if ( selection && jQuery.inArray( elem, selection ) > -1 ) { + if ( ignored ) { + ignored.push( elem ); + } + continue; + } + + attached = isAttached( elem ); + + // Append to fragment + tmp = getAll( fragment.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( attached ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( ( elem = tmp[ j++ ] ) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + return fragment; +} + + +var rtypenamespace = /^([^.]*)(?:\.(.+)|)/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +// Support: IE <=9 - 11+ +// focus() and blur() are asynchronous, except when they are no-op. +// So expect focus to be synchronous when the element is already active, +// and blur to be synchronous when the element is not already active. +// (focus and blur are always synchronous in other supported browsers, +// this just defines when we can count on it). +function expectSync( elem, type ) { + return ( elem === safeActiveElement() ) === ( type === "focus" ); +} + +// Support: IE <=9 only +// Accessing document.activeElement can throw unexpectedly +// https://bugs.jquery.com/ticket/13393 +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +function on( elem, types, selector, data, fn, one ) { + var origFn, type; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + on( elem, type, selector, data, types[ type ], one ); + } + return elem; + } + + if ( data == null && fn == null ) { + + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return elem; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return elem.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + } ); +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + + var handleObjIn, eventHandle, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.get( elem ); + + // Only attach events to objects that accept data + if ( !acceptData( elem ) ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Ensure that invalid selectors throw exceptions at attach time + // Evaluate against documentElement in case elem is a non-element node (e.g., document) + if ( selector ) { + jQuery.find.matchesSelector( documentElement, selector ); + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !( events = elemData.events ) ) { + events = elemData.events = Object.create( null ); + } + if ( !( eventHandle = elemData.handle ) ) { + eventHandle = elemData.handle = function( e ) { + + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? + jQuery.event.dispatch.apply( elem, arguments ) : undefined; + }; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend( { + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join( "." ) + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !( handlers = events[ type ] ) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener if the special events handler returns false + if ( !special.setup || + special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + + var j, origCount, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); + + if ( !elemData || !( events = elemData.events ) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[ 2 ] && + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || + selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || + special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove data and the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + dataPriv.remove( elem, "handle events" ); + } + }, + + dispatch: function( nativeEvent ) { + + var i, j, ret, matched, handleObj, handlerQueue, + args = new Array( arguments.length ), + + // Make a writable jQuery.Event from the native event object + event = jQuery.event.fix( nativeEvent ), + + handlers = ( + dataPriv.get( this, "events" ) || Object.create( null ) + )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[ 0 ] = event; + + for ( i = 1; i < arguments.length; i++ ) { + args[ i ] = arguments[ i ]; + } + + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( ( handleObj = matched.handlers[ j++ ] ) && + !event.isImmediatePropagationStopped() ) { + + // If the event is namespaced, then each handler is only invoked if it is + // specially universal or its namespaces are a superset of the event's. + if ( !event.rnamespace || handleObj.namespace === false || + event.rnamespace.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || + handleObj.handler ).apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( ( event.result = ret ) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var i, handleObj, sel, matchedHandlers, matchedSelectors, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + if ( delegateCount && + + // Support: IE <=9 + // Black-hole SVG instance trees (trac-13180) + cur.nodeType && + + // Support: Firefox <=42 + // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) + // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click + // Support: IE 11 only + // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) + !( event.type === "click" && event.button >= 1 ) ) { + + for ( ; cur !== this; cur = cur.parentNode || this ) { + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { + matchedHandlers = []; + matchedSelectors = {}; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matchedSelectors[ sel ] === undefined ) { + matchedSelectors[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) > -1 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matchedSelectors[ sel ] ) { + matchedHandlers.push( handleObj ); + } + } + if ( matchedHandlers.length ) { + handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); + } + } + } + } + + // Add the remaining (directly-bound) handlers + cur = this; + if ( delegateCount < handlers.length ) { + handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); + } + + return handlerQueue; + }, + + addProp: function( name, hook ) { + Object.defineProperty( jQuery.Event.prototype, name, { + enumerable: true, + configurable: true, + + get: isFunction( hook ) ? + function() { + if ( this.originalEvent ) { + return hook( this.originalEvent ); + } + } : + function() { + if ( this.originalEvent ) { + return this.originalEvent[ name ]; + } + }, + + set: function( value ) { + Object.defineProperty( this, name, { + enumerable: true, + configurable: true, + writable: true, + value: value + } ); + } + } ); + }, + + fix: function( originalEvent ) { + return originalEvent[ jQuery.expando ] ? + originalEvent : + new jQuery.Event( originalEvent ); + }, + + special: { + load: { + + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + click: { + + // Utilize native event to ensure correct state for checkable inputs + setup: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Claim the first handler + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + // dataPriv.set( el, "click", ... ) + leverageNative( el, "click", returnTrue ); + } + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Force setup before triggering a click + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + leverageNative( el, "click" ); + } + + // Return non-false to allow normal event-path propagation + return true; + }, + + // For cross-browser consistency, suppress native .click() on links + // Also prevent it if we're currently inside a leveraged native-event stack + _default: function( event ) { + var target = event.target; + return rcheckableType.test( target.type ) && + target.click && nodeName( target, "input" ) && + dataPriv.get( target, "click" ) || + nodeName( target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + } +}; + +// Ensure the presence of an event listener that handles manually-triggered +// synthetic events by interrupting progress until reinvoked in response to +// *native* events that it fires directly, ensuring that state changes have +// already occurred before other listeners are invoked. +function leverageNative( el, type, expectSync ) { + + // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add + if ( !expectSync ) { + if ( dataPriv.get( el, type ) === undefined ) { + jQuery.event.add( el, type, returnTrue ); + } + return; + } + + // Register the controller as a special universal handler for all event namespaces + dataPriv.set( el, type, false ); + jQuery.event.add( el, type, { + namespace: false, + handler: function( event ) { + var notAsync, result, + saved = dataPriv.get( this, type ); + + if ( ( event.isTrigger & 1 ) && this[ type ] ) { + + // Interrupt processing of the outer synthetic .trigger()ed event + // Saved data should be false in such cases, but might be a leftover capture object + // from an async native handler (gh-4350) + if ( !saved.length ) { + + // Store arguments for use when handling the inner native event + // There will always be at least one argument (an event object), so this array + // will not be confused with a leftover capture object. + saved = slice.call( arguments ); + dataPriv.set( this, type, saved ); + + // Trigger the native event and capture its result + // Support: IE <=9 - 11+ + // focus() and blur() are asynchronous + notAsync = expectSync( this, type ); + this[ type ](); + result = dataPriv.get( this, type ); + if ( saved !== result || notAsync ) { + dataPriv.set( this, type, false ); + } else { + result = {}; + } + if ( saved !== result ) { + + // Cancel the outer synthetic event + event.stopImmediatePropagation(); + event.preventDefault(); + + // Support: Chrome 86+ + // In Chrome, if an element having a focusout handler is blurred by + // clicking outside of it, it invokes the handler synchronously. If + // that handler calls `.remove()` on the element, the data is cleared, + // leaving `result` undefined. We need to guard against this. + return result && result.value; + } + + // If this is an inner synthetic event for an event with a bubbling surrogate + // (focus or blur), assume that the surrogate already propagated from triggering the + // native event and prevent that from happening again here. + // This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the + // bubbling surrogate propagates *after* the non-bubbling base), but that seems + // less bad than duplication. + } else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) { + event.stopPropagation(); + } + + // If this is a native event triggered above, everything is now in order + // Fire an inner synthetic event with the original arguments + } else if ( saved.length ) { + + // ...and capture the result + dataPriv.set( this, type, { + value: jQuery.event.trigger( + + // Support: IE <=9 - 11+ + // Extend with the prototype to reset the above stopImmediatePropagation() + jQuery.extend( saved[ 0 ], jQuery.Event.prototype ), + saved.slice( 1 ), + this + ) + } ); + + // Abort handling of the native event + event.stopImmediatePropagation(); + } + } + } ); +} + +jQuery.removeEvent = function( elem, type, handle ) { + + // This "if" is needed for plain objects + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle ); + } +}; + +jQuery.Event = function( src, props ) { + + // Allow instantiation without the 'new' keyword + if ( !( this instanceof jQuery.Event ) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + + // Support: Android <=2.3 only + src.returnValue === false ? + returnTrue : + returnFalse; + + // Create target properties + // Support: Safari <=6 - 7 only + // Target should not be a text node (#504, #13143) + this.target = ( src.target && src.target.nodeType === 3 ) ? + src.target.parentNode : + src.target; + + this.currentTarget = src.currentTarget; + this.relatedTarget = src.relatedTarget; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || Date.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + constructor: jQuery.Event, + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + isSimulated: false, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + + if ( e && !this.isSimulated ) { + e.preventDefault(); + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopPropagation(); + } + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Includes all common event props including KeyEvent and MouseEvent specific props +jQuery.each( { + altKey: true, + bubbles: true, + cancelable: true, + changedTouches: true, + ctrlKey: true, + detail: true, + eventPhase: true, + metaKey: true, + pageX: true, + pageY: true, + shiftKey: true, + view: true, + "char": true, + code: true, + charCode: true, + key: true, + keyCode: true, + button: true, + buttons: true, + clientX: true, + clientY: true, + offsetX: true, + offsetY: true, + pointerId: true, + pointerType: true, + screenX: true, + screenY: true, + targetTouches: true, + toElement: true, + touches: true, + which: true +}, jQuery.event.addProp ); + +jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) { + jQuery.event.special[ type ] = { + + // Utilize native event if possible so blur/focus sequence is correct + setup: function() { + + // Claim the first handler + // dataPriv.set( this, "focus", ... ) + // dataPriv.set( this, "blur", ... ) + leverageNative( this, type, expectSync ); + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function() { + + // Force setup before trigger + leverageNative( this, type ); + + // Return non-false to allow normal event-path propagation + return true; + }, + + // Suppress native focus or blur as it's already being fired + // in leverageNative. + _default: function() { + return true; + }, + + delegateType: delegateType + }; +} ); + +// Create mouseenter/leave events using mouseover/out and event-time checks +// so that event delegation works in jQuery. +// Do the same for pointerenter/pointerleave and pointerover/pointerout +// +// Support: Safari 7 only +// Safari sends mouseenter too often; see: +// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 +// for the description of the bug (it existed in older Chrome versions as well). +jQuery.each( { + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mouseenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +} ); + +jQuery.fn.extend( { + + on: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn ); + }, + one: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? + handleObj.origType + "." + handleObj.namespace : + handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each( function() { + jQuery.event.remove( this, types, fn, selector ); + } ); + } +} ); + + +var + + // Support: IE <=10 - 11, Edge 12 - 13 only + // In IE/Edge using regex groups here causes severe slowdowns. + // See https://connect.microsoft.com/IE/feedback/details/1736512/ + rnoInnerhtml = /\s*$/g; + +// Prefer a tbody over its parent table for containing new rows +function manipulationTarget( elem, content ) { + if ( nodeName( elem, "table" ) && + nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { + + return jQuery( elem ).children( "tbody" )[ 0 ] || elem; + } + + return elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) { + elem.type = elem.type.slice( 5 ); + } else { + elem.removeAttribute( "type" ); + } + + return elem; +} + +function cloneCopyEvent( src, dest ) { + var i, l, type, pdataOld, udataOld, udataCur, events; + + if ( dest.nodeType !== 1 ) { + return; + } + + // 1. Copy private data: events, handlers, etc. + if ( dataPriv.hasData( src ) ) { + pdataOld = dataPriv.get( src ); + events = pdataOld.events; + + if ( events ) { + dataPriv.remove( dest, "handle events" ); + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + } + + // 2. Copy user data + if ( dataUser.hasData( src ) ) { + udataOld = dataUser.access( src ); + udataCur = jQuery.extend( {}, udataOld ); + + dataUser.set( dest, udataCur ); + } +} + +// Fix IE bugs, see support tests +function fixInput( src, dest ) { + var nodeName = dest.nodeName.toLowerCase(); + + // Fails to persist the checked state of a cloned checkbox or radio button. + if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + dest.checked = src.checked; + + // Fails to return the selected option to the default selected state when cloning options + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +function domManip( collection, args, callback, ignored ) { + + // Flatten any nested arrays + args = flat( args ); + + var fragment, first, scripts, hasScripts, node, doc, + i = 0, + l = collection.length, + iNoClone = l - 1, + value = args[ 0 ], + valueIsFunction = isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( valueIsFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return collection.each( function( index ) { + var self = collection.eq( index ); + if ( valueIsFunction ) { + args[ 0 ] = value.call( this, index, self.html() ); + } + domManip( self, args, callback, ignored ); + } ); + } + + if ( l ) { + fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + // Require either new content or an interest in ignored elements to invoke the callback + if ( first || ignored ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item + // instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( collection[ i ], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !dataPriv.access( node, "globalEval" ) && + jQuery.contains( doc, node ) ) { + + if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) { + + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl && !node.noModule ) { + jQuery._evalUrl( node.src, { + nonce: node.nonce || node.getAttribute( "nonce" ) + }, doc ); + } + } else { + DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc ); + } + } + } + } + } + } + + return collection; +} + +function remove( elem, selector, keepData ) { + var node, + nodes = selector ? jQuery.filter( selector, elem ) : elem, + i = 0; + + for ( ; ( node = nodes[ i ] ) != null; i++ ) { + if ( !keepData && node.nodeType === 1 ) { + jQuery.cleanData( getAll( node ) ); + } + + if ( node.parentNode ) { + if ( keepData && isAttached( node ) ) { + setGlobalEval( getAll( node, "script" ) ); + } + node.parentNode.removeChild( node ); + } + } + + return elem; +} + +jQuery.extend( { + htmlPrefilter: function( html ) { + return html; + }, + + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var i, l, srcElements, destElements, + clone = elem.cloneNode( true ), + inPage = isAttached( elem ); + + // Fix IE cloning issues + if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && + !jQuery.isXMLDoc( elem ) ) { + + // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + fixInput( srcElements[ i ], destElements[ i ] ); + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + cloneCopyEvent( srcElements[ i ], destElements[ i ] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + // Return the cloned set + return clone; + }, + + cleanData: function( elems ) { + var data, elem, type, + special = jQuery.event.special, + i = 0; + + for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { + if ( acceptData( elem ) ) { + if ( ( data = elem[ dataPriv.expando ] ) ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataPriv.expando ] = undefined; + } + if ( elem[ dataUser.expando ] ) { + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataUser.expando ] = undefined; + } + } + } + } +} ); + +jQuery.fn.extend( { + detach: function( selector ) { + return remove( this, selector, true ); + }, + + remove: function( selector ) { + return remove( this, selector ); + }, + + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().each( function() { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + this.textContent = value; + } + } ); + }, null, value, arguments.length ); + }, + + append: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + } ); + }, + + prepend: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + } ); + }, + + before: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + } ); + }, + + after: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + } ); + }, + + empty: function() { + var elem, + i = 0; + + for ( ; ( elem = this[ i ] ) != null; i++ ) { + if ( elem.nodeType === 1 ) { + + // Prevent memory leaks + jQuery.cleanData( getAll( elem, false ) ); + + // Remove any remaining nodes + elem.textContent = ""; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map( function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + } ); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined && elem.nodeType === 1 ) { + return elem.innerHTML; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { + + value = jQuery.htmlPrefilter( value ); + + try { + for ( ; i < l; i++ ) { + elem = this[ i ] || {}; + + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch ( e ) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var ignored = []; + + // Make the changes, replacing each non-ignored context element with the new content + return domManip( this, arguments, function( elem ) { + var parent = this.parentNode; + + if ( jQuery.inArray( this, ignored ) < 0 ) { + jQuery.cleanData( getAll( this ) ); + if ( parent ) { + parent.replaceChild( elem, this ); + } + } + + // Force callback invocation + }, ignored ); + } +} ); + +jQuery.each( { + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1, + i = 0; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone( true ); + jQuery( insert[ i ] )[ original ]( elems ); + + // Support: Android <=4.0 only, PhantomJS 1 only + // .get() because push.apply(_, arraylike) throws on ancient WebKit + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +} ); +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + +var getStyles = function( elem ) { + + // Support: IE <=11 only, Firefox <=30 (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + var view = elem.ownerDocument.defaultView; + + if ( !view || !view.opener ) { + view = window; + } + + return view.getComputedStyle( elem ); + }; + +var swap = function( elem, options, callback ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.call( elem ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + +var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" ); + + + +( function() { + + // Executing both pixelPosition & boxSizingReliable tests require only one layout + // so they're executed at the same time to save the second computation. + function computeStyleTests() { + + // This is a singleton, we need to execute it only once + if ( !div ) { + return; + } + + container.style.cssText = "position:absolute;left:-11111px;width:60px;" + + "margin-top:1px;padding:0;border:0"; + div.style.cssText = + "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + + "margin:auto;border:1px;padding:1px;" + + "width:60%;top:1%"; + documentElement.appendChild( container ).appendChild( div ); + + var divStyle = window.getComputedStyle( div ); + pixelPositionVal = divStyle.top !== "1%"; + + // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 + reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12; + + // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 + // Some styles come back with percentage values, even though they shouldn't + div.style.right = "60%"; + pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36; + + // Support: IE 9 - 11 only + // Detect misreporting of content dimensions for box-sizing:border-box elements + boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36; + + // Support: IE 9 only + // Detect overflow:scroll screwiness (gh-3699) + // Support: Chrome <=64 + // Don't get tricked when zoom affects offsetWidth (gh-4029) + div.style.position = "absolute"; + scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12; + + documentElement.removeChild( container ); + + // Nullify the div so it wouldn't be stored in the memory and + // it will also be a sign that checks already performed + div = null; + } + + function roundPixelMeasures( measure ) { + return Math.round( parseFloat( measure ) ); + } + + var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, + reliableTrDimensionsVal, reliableMarginLeftVal, + container = document.createElement( "div" ), + div = document.createElement( "div" ); + + // Finish early in limited (non-browser) environments + if ( !div.style ) { + return; + } + + // Support: IE <=9 - 11 only + // Style of cloned element affects source element cloned (#8908) + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + jQuery.extend( support, { + boxSizingReliable: function() { + computeStyleTests(); + return boxSizingReliableVal; + }, + pixelBoxStyles: function() { + computeStyleTests(); + return pixelBoxStylesVal; + }, + pixelPosition: function() { + computeStyleTests(); + return pixelPositionVal; + }, + reliableMarginLeft: function() { + computeStyleTests(); + return reliableMarginLeftVal; + }, + scrollboxSize: function() { + computeStyleTests(); + return scrollboxSizeVal; + }, + + // Support: IE 9 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Behavior in IE 9 is more subtle than in newer versions & it passes + // some versions of this test; make sure not to make it pass there! + // + // Support: Firefox 70+ + // Only Firefox includes border widths + // in computed dimensions. (gh-4529) + reliableTrDimensions: function() { + var table, tr, trChild, trStyle; + if ( reliableTrDimensionsVal == null ) { + table = document.createElement( "table" ); + tr = document.createElement( "tr" ); + trChild = document.createElement( "div" ); + + table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate"; + tr.style.cssText = "border:1px solid"; + + // Support: Chrome 86+ + // Height set through cssText does not get applied. + // Computed height then comes back as 0. + tr.style.height = "1px"; + trChild.style.height = "9px"; + + // Support: Android 8 Chrome 86+ + // In our bodyBackground.html iframe, + // display for all div elements is set to "inline", + // which causes a problem only in Android 8 Chrome 86. + // Ensuring the div is display: block + // gets around this issue. + trChild.style.display = "block"; + + documentElement + .appendChild( table ) + .appendChild( tr ) + .appendChild( trChild ); + + trStyle = window.getComputedStyle( tr ); + reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) + + parseInt( trStyle.borderTopWidth, 10 ) + + parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight; + + documentElement.removeChild( table ); + } + return reliableTrDimensionsVal; + } + } ); +} )(); + + +function curCSS( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + + // Support: Firefox 51+ + // Retrieving style before computed somehow + // fixes an issue with getting wrong values + // on detached elements + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is needed for: + // .css('filter') (IE 9 only, #12537) + // .css('--customProperty) (#3144) + if ( computed ) { + ret = computed.getPropertyValue( name ) || computed[ name ]; + + if ( ret === "" && !isAttached( elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Android Browser returns percentage for some values, + // but width seems to be reliably pixels. + // This is against the CSSOM draft spec: + // https://drafts.csswg.org/cssom/#resolved-values + if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + return ret !== undefined ? + + // Support: IE <=9 - 11 only + // IE returns zIndex value as an integer. + ret + "" : + ret; +} + + +function addGetHookIf( conditionFn, hookFn ) { + + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + if ( conditionFn() ) { + + // Hook not needed (or it's not possible to use it due + // to missing dependency), remove it. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + return ( this.get = hookFn ).apply( this, arguments ); + } + }; +} + + +var cssPrefixes = [ "Webkit", "Moz", "ms" ], + emptyStyle = document.createElement( "div" ).style, + vendorProps = {}; + +// Return a vendor-prefixed property or undefined +function vendorPropName( name ) { + + // Check for vendor prefixed names + var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in emptyStyle ) { + return name; + } + } +} + +// Return a potentially-mapped jQuery.cssProps or vendor prefixed property +function finalPropName( name ) { + var final = jQuery.cssProps[ name ] || vendorProps[ name ]; + + if ( final ) { + return final; + } + if ( name in emptyStyle ) { + return name; + } + return vendorProps[ name ] = vendorPropName( name ) || name; +} + + +var + + // Swappable if display is none or starts with table + // except "table", "table-cell", or "table-caption" + // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rcustomProp = /^--/, + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }; + +function setPositiveNumber( _elem, value, subtract ) { + + // Any relative (+/-) values have already been + // normalized at this point + var matches = rcssNum.exec( value ); + return matches ? + + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : + value; +} + +function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) { + var i = dimension === "width" ? 1 : 0, + extra = 0, + delta = 0; + + // Adjustment may not be necessary + if ( box === ( isBorderBox ? "border" : "content" ) ) { + return 0; + } + + for ( ; i < 4; i += 2 ) { + + // Both box models exclude margin + if ( box === "margin" ) { + delta += jQuery.css( elem, box + cssExpand[ i ], true, styles ); + } + + // If we get here with a content-box, we're seeking "padding" or "border" or "margin" + if ( !isBorderBox ) { + + // Add padding + delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // For "border" or "margin", add border + if ( box !== "padding" ) { + delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + + // But still keep track of it otherwise + } else { + extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + + // If we get here with a border-box (content + padding + border), we're seeking "content" or + // "padding" or "margin" + } else { + + // For "content", subtract padding + if ( box === "content" ) { + delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // For "content" or "padding", subtract border + if ( box !== "margin" ) { + delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + // Account for positive content-box scroll gutter when requested by providing computedVal + if ( !isBorderBox && computedVal >= 0 ) { + + // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border + // Assuming integer scroll gutter, subtract the rest and round down + delta += Math.max( 0, Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + computedVal - + delta - + extra - + 0.5 + + // If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter + // Use an explicit zero to avoid NaN (gh-3964) + ) ) || 0; + } + + return delta; +} + +function getWidthOrHeight( elem, dimension, extra ) { + + // Start with computed style + var styles = getStyles( elem ), + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322). + // Fake content-box until we know it's needed to know the true value. + boxSizingNeeded = !support.boxSizingReliable() || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + valueIsBorderBox = isBorderBox, + + val = curCSS( elem, dimension, styles ), + offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ); + + // Support: Firefox <=54 + // Return a confounding non-pixel value or feign ignorance, as appropriate. + if ( rnumnonpx.test( val ) ) { + if ( !extra ) { + return val; + } + val = "auto"; + } + + + // Support: IE 9 - 11 only + // Use offsetWidth/offsetHeight for when box sizing is unreliable. + // In those cases, the computed value can be trusted to be border-box. + if ( ( !support.boxSizingReliable() && isBorderBox || + + // Support: IE 10 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Interestingly, in some cases IE 9 doesn't suffer from this issue. + !support.reliableTrDimensions() && nodeName( elem, "tr" ) || + + // Fall back to offsetWidth/offsetHeight when value is "auto" + // This happens for inline elements with no explicit setting (gh-3571) + val === "auto" || + + // Support: Android <=4.1 - 4.3 only + // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) + !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) && + + // Make sure the element is visible & connected + elem.getClientRects().length ) { + + isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // Where available, offsetWidth/offsetHeight approximate border box dimensions. + // Where not available (e.g., SVG), assume unreliable box-sizing and interpret the + // retrieved value as a content box dimension. + valueIsBorderBox = offsetProp in elem; + if ( valueIsBorderBox ) { + val = elem[ offsetProp ]; + } + } + + // Normalize "" and auto + val = parseFloat( val ) || 0; + + // Adjust for the element's box model + return ( val + + boxModelAdjustment( + elem, + dimension, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles, + + // Provide the current computed size to request scroll gutter calculation (gh-3589) + val + ) + ) + "px"; +} + +jQuery.extend( { + + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "animationIterationCount": true, + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "gridArea": true, + "gridColumn": true, + "gridColumnEnd": true, + "gridColumnStart": true, + "gridRow": true, + "gridRowEnd": true, + "gridRowStart": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: {}, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ), + style = elem.style; + + // Make sure that we're working with the right name. We don't + // want to query the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Gets hook for the prefixed version, then unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // Convert "+=" or "-=" to relative numbers (#7345) + if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { + value = adjustCSS( elem, name, ret ); + + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set (#7116) + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add the unit (except for certain CSS properties) + // The isCustomProp check can be removed in jQuery 4.0 when we only auto-append + // "px" to a few hardcoded values. + if ( type === "number" && !isCustomProp ) { + value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); + } + + // background-* props affect original clone's values + if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !( "set" in hooks ) || + ( value = hooks.set( elem, value, extra ) ) !== undefined ) { + + if ( isCustomProp ) { + style.setProperty( name, value ); + } else { + style[ name ] = value; + } + } + + } else { + + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && + ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { + + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var val, num, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ); + + // Make sure that we're working with the right name. We don't + // want to modify the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Try prefixed name followed by the unprefixed name + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + // Convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Make numeric if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || isFinite( num ) ? num || 0 : val; + } + + return val; + } +} ); + +jQuery.each( [ "height", "width" ], function( _i, dimension ) { + jQuery.cssHooks[ dimension ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + + // Certain elements can have dimension info if we invisibly show them + // but it must have a current display style that would benefit + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && + + // Support: Safari 8+ + // Table columns in Safari have non-zero offsetWidth & zero + // getBoundingClientRect().width unless display is changed. + // Support: IE <=11 only + // Running getBoundingClientRect on a disconnected node + // in IE throws an error. + ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? + swap( elem, cssShow, function() { + return getWidthOrHeight( elem, dimension, extra ); + } ) : + getWidthOrHeight( elem, dimension, extra ); + } + }, + + set: function( elem, value, extra ) { + var matches, + styles = getStyles( elem ), + + // Only read styles.position if the test has a chance to fail + // to avoid forcing a reflow. + scrollboxSizeBuggy = !support.scrollboxSize() && + styles.position === "absolute", + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991) + boxSizingNeeded = scrollboxSizeBuggy || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + subtract = extra ? + boxModelAdjustment( + elem, + dimension, + extra, + isBorderBox, + styles + ) : + 0; + + // Account for unreliable border-box dimensions by comparing offset* to computed and + // faking a content-box to get border and padding (gh-3699) + if ( isBorderBox && scrollboxSizeBuggy ) { + subtract -= Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + parseFloat( styles[ dimension ] ) - + boxModelAdjustment( elem, dimension, "border", false, styles ) - + 0.5 + ); + } + + // Convert to pixels if value adjustment is needed + if ( subtract && ( matches = rcssNum.exec( value ) ) && + ( matches[ 3 ] || "px" ) !== "px" ) { + + elem.style[ dimension ] = value; + value = jQuery.css( elem, dimension ); + } + + return setPositiveNumber( elem, value, subtract ); + } + }; +} ); + +jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, + function( elem, computed ) { + if ( computed ) { + return ( parseFloat( curCSS( elem, "marginLeft" ) ) || + elem.getBoundingClientRect().left - + swap( elem, { marginLeft: 0 }, function() { + return elem.getBoundingClientRect().left; + } ) + ) + "px"; + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each( { + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // Assumes a single number if not a string + parts = typeof value === "string" ? value.split( " " ) : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( prefix !== "margin" ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +} ); + +jQuery.fn.extend( { + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( Array.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + } +} ); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || jQuery.easing._default; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + // Use a property on the element directly when it is not a DOM element, + // or when there is no matching style property that exists. + if ( tween.elem.nodeType !== 1 || + tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { + return tween.elem[ tween.prop ]; + } + + // Passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails. + // Simple values such as "10px" are parsed to Float; + // complex values such as "rotate(1rad)" are returned as-is. + result = jQuery.css( tween.elem, tween.prop, "" ); + + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + + // Use step hook for back compat. + // Use cssHook if its there. + // Use .style if available and use plain properties where available. + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.nodeType === 1 && ( + jQuery.cssHooks[ tween.prop ] || + tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 only +// Panic based approach to setting things on disconnected nodes +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + }, + _default: "swing" +}; + +jQuery.fx = Tween.prototype.init; + +// Back compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, inProgress, + rfxtypes = /^(?:toggle|show|hide)$/, + rrun = /queueHooks$/; + +function schedule() { + if ( inProgress ) { + if ( document.hidden === false && window.requestAnimationFrame ) { + window.requestAnimationFrame( schedule ); + } else { + window.setTimeout( schedule, jQuery.fx.interval ); + } + + jQuery.fx.tick(); + } +} + +// Animations created synchronously will run synchronously +function createFxNow() { + window.setTimeout( function() { + fxNow = undefined; + } ); + return ( fxNow = Date.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + i = 0, + attrs = { height: type }; + + // If we include width, step value is 1 to do all cssExpand values, + // otherwise step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { + + // We're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, + isBox = "width" in props || "height" in props, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHiddenWithinTree( elem ), + dataShow = dataPriv.get( elem, "fxshow" ); + + // Queue-skipping animations hijack the fx hooks + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always( function() { + + // Ensure the complete handler is called before this completes + anim.always( function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + } ); + } ); + } + + // Detect show/hide animations + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.test( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // Pretend to be hidden if this is a "show" and + // there is still data from a stopped show/hide + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + + // Ignore all other no-op show/hide data + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + } + } + + // Bail out if this is a no-op like .hide().hide() + propTween = !jQuery.isEmptyObject( props ); + if ( !propTween && jQuery.isEmptyObject( orig ) ) { + return; + } + + // Restrict "overflow" and "display" styles during box animations + if ( isBox && elem.nodeType === 1 ) { + + // Support: IE <=9 - 11, Edge 12 - 15 + // Record all 3 overflow attributes because IE does not infer the shorthand + // from identically-valued overflowX and overflowY and Edge just mirrors + // the overflowX value there. + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Identify a display type, preferring old show/hide data over the CSS cascade + restoreDisplay = dataShow && dataShow.display; + if ( restoreDisplay == null ) { + restoreDisplay = dataPriv.get( elem, "display" ); + } + display = jQuery.css( elem, "display" ); + if ( display === "none" ) { + if ( restoreDisplay ) { + display = restoreDisplay; + } else { + + // Get nonempty value(s) by temporarily forcing visibility + showHide( [ elem ], true ); + restoreDisplay = elem.style.display || restoreDisplay; + display = jQuery.css( elem, "display" ); + showHide( [ elem ] ); + } + } + + // Animate inline elements as inline-block + if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { + if ( jQuery.css( elem, "float" ) === "none" ) { + + // Restore the original display value at the end of pure show/hide animations + if ( !propTween ) { + anim.done( function() { + style.display = restoreDisplay; + } ); + if ( restoreDisplay == null ) { + display = style.display; + restoreDisplay = display === "none" ? "" : display; + } + } + style.display = "inline-block"; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + anim.always( function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + } ); + } + + // Implement show/hide animations + propTween = false; + for ( prop in orig ) { + + // General show/hide setup for this element animation + if ( !propTween ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); + } + + // Store hidden/visible for toggle so `.stop().toggle()` "reverses" + if ( toggle ) { + dataShow.hidden = !hidden; + } + + // Show elements before animating them + if ( hidden ) { + showHide( [ elem ], true ); + } + + /* eslint-disable no-loop-func */ + + anim.done( function() { + + /* eslint-enable no-loop-func */ + + // The final step of a "hide" animation is actually hiding the element + if ( !hidden ) { + showHide( [ elem ] ); + } + dataPriv.remove( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + } ); + } + + // Per-property setup + propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = propTween.start; + if ( hidden ) { + propTween.end = propTween.start; + propTween.start = 0; + } + } + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( Array.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // Not quite $.extend, this won't overwrite existing keys. + // Reusing 'index' because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = Animation.prefilters.length, + deferred = jQuery.Deferred().always( function() { + + // Don't match elem in the :animated selector + delete tick.elem; + } ), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + + // Support: Android 2.3 only + // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ] ); + + // If there's more to do, yield + if ( percent < 1 && length ) { + return remaining; + } + + // If this was an empty animation, synthesize a final progress notification + if ( !length ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + } + + // Resolve the animation and report its conclusion + deferred.resolveWith( elem, [ animation ] ); + return false; + }, + animation = deferred.promise( { + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { + specialEasing: {}, + easing: jQuery.easing._default + }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + + // If we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // Resolve when we played the last frame; otherwise, reject + if ( gotoEnd ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + } ), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length; index++ ) { + result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + if ( isFunction( result.stop ) ) { + jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = + result.stop.bind( result ); + } + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + // Attach callbacks from options + animation + .progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + } ) + ); + + return animation; +} + +jQuery.Animation = jQuery.extend( Animation, { + + tweeners: { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ); + adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); + return tween; + } ] + }, + + tweener: function( props, callback ) { + if ( isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.match( rnothtmlwhite ); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length; index++ ) { + prop = props[ index ]; + Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; + Animation.tweeners[ prop ].unshift( callback ); + } + }, + + prefilters: [ defaultPrefilter ], + + prefilter: function( callback, prepend ) { + if ( prepend ) { + Animation.prefilters.unshift( callback ); + } else { + Animation.prefilters.push( callback ); + } + } +} ); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !isFunction( easing ) && easing + }; + + // Go to the end state if fx are off + if ( jQuery.fx.off ) { + opt.duration = 0; + + } else { + if ( typeof opt.duration !== "number" ) { + if ( opt.duration in jQuery.fx.speeds ) { + opt.duration = jQuery.fx.speeds[ opt.duration ]; + + } else { + opt.duration = jQuery.fx.speeds._default; + } + } + } + + // Normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend( { + fadeTo: function( speed, to, easing, callback ) { + + // Show any hidden elements after setting opacity to 0 + return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() + + // Animate to the value specified + .end().animate( { opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || dataPriv.get( this, "finish" ) ) { + anim.stop( true ); + } + }; + + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue ) { + this.queue( type || "fx", [] ); + } + + return this.each( function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = dataPriv.get( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && + ( type == null || timers[ index ].queue === type ) ) { + + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // Start the next in the queue if the last step wasn't forced. + // Timers currently will call their complete callbacks, which + // will dequeue but only if they were gotoEnd. + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + } ); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each( function() { + var index, + data = dataPriv.get( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // Enable finishing flag on private data + data.finish = true; + + // Empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // Look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // Look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // Turn off finishing flag + delete data.finish; + } ); + } +} ); + +jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +} ); + +// Generate shortcuts for custom animations +jQuery.each( { + slideDown: genFx( "show" ), + slideUp: genFx( "hide" ), + slideToggle: genFx( "toggle" ), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +} ); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + i = 0, + timers = jQuery.timers; + + fxNow = Date.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + + // Run the timer and safely remove it when done (allowing for external removal) + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + jQuery.fx.start(); +}; + +jQuery.fx.interval = 13; +jQuery.fx.start = function() { + if ( inProgress ) { + return; + } + + inProgress = true; + schedule(); +}; + +jQuery.fx.stop = function() { + inProgress = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = window.setTimeout( next, time ); + hooks.stop = function() { + window.clearTimeout( timeout ); + }; + } ); +}; + + +( function() { + var input = document.createElement( "input" ), + select = document.createElement( "select" ), + opt = select.appendChild( document.createElement( "option" ) ); + + input.type = "checkbox"; + + // Support: Android <=4.3 only + // Default value for a checkbox should be "on" + support.checkOn = input.value !== ""; + + // Support: IE <=11 only + // Must access selectedIndex to make default options select + support.optSelected = opt.selected; + + // Support: IE <=11 only + // An input loses its value after becoming a radio + input = document.createElement( "input" ); + input.value = "t"; + input.type = "radio"; + support.radioValue = input.value === "t"; +} )(); + + +var boolHook, + attrHandle = jQuery.expr.attrHandle; + +jQuery.fn.extend( { + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each( function() { + jQuery.removeAttr( this, name ); + } ); + } +} ); + +jQuery.extend( { + attr: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set attributes on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === "undefined" ) { + return jQuery.prop( elem, name, value ); + } + + // Attribute hooks are determined by the lowercase version + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + hooks = jQuery.attrHooks[ name.toLowerCase() ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); + } + + if ( value !== undefined ) { + if ( value === null ) { + jQuery.removeAttr( elem, name ); + return; + } + + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + elem.setAttribute( name, value + "" ); + return value; + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? undefined : ret; + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && + nodeName( elem, "input" ) ) { + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + }, + + removeAttr: function( elem, value ) { + var name, + i = 0, + + // Attribute names can contain non-HTML whitespace characters + // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 + attrNames = value && value.match( rnothtmlwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( ( name = attrNames[ i++ ] ) ) { + elem.removeAttribute( name ); + } + } + } +} ); + +// Hooks for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + elem.setAttribute( name, name ); + } + return name; + } +}; + +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) { + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = function( elem, name, isXML ) { + var ret, handle, + lowercaseName = name.toLowerCase(); + + if ( !isXML ) { + + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ lowercaseName ]; + attrHandle[ lowercaseName ] = ret; + ret = getter( elem, name, isXML ) != null ? + lowercaseName : + null; + attrHandle[ lowercaseName ] = handle; + } + return ret; + }; +} ); + + + + +var rfocusable = /^(?:input|select|textarea|button)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend( { + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + return this.each( function() { + delete this[ jQuery.propFix[ name ] || name ]; + } ); + } +} ); + +jQuery.extend( { + prop: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set properties on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + return ( elem[ name ] = value ); + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + return elem[ name ]; + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + + // Support: IE <=9 - 11 only + // elem.tabIndex doesn't always return the + // correct value when it hasn't been explicitly set + // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + if ( tabindex ) { + return parseInt( tabindex, 10 ); + } + + if ( + rfocusable.test( elem.nodeName ) || + rclickable.test( elem.nodeName ) && + elem.href + ) { + return 0; + } + + return -1; + } + } + }, + + propFix: { + "for": "htmlFor", + "class": "className" + } +} ); + +// Support: IE <=11 only +// Accessing the selectedIndex property +// forces the browser to respect setting selected +// on the option +// The getter ensures a default option is selected +// when in an optgroup +// eslint rule "no-unused-expressions" is disabled for this code +// since it considers such accessions noop +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent && parent.parentNode ) { + parent.parentNode.selectedIndex; + } + return null; + }, + set: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + }; +} + +jQuery.each( [ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +} ); + + + + + // Strip and collapse whitespace according to HTML spec + // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace + function stripAndCollapse( value ) { + var tokens = value.match( rnothtmlwhite ) || []; + return tokens.join( " " ); + } + + +function getClass( elem ) { + return elem.getAttribute && elem.getAttribute( "class" ) || ""; +} + +function classesToArray( value ) { + if ( Array.isArray( value ) ) { + return value; + } + if ( typeof value === "string" ) { + return value.match( rnothtmlwhite ) || []; + } + return []; +} + +jQuery.fn.extend( { + addClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( !arguments.length ) { + return this.attr( "class", "" ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) > -1 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value, + isValidValue = type === "string" || Array.isArray( value ); + + if ( typeof stateVal === "boolean" && isValidValue ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( isFunction( value ) ) { + return this.each( function( i ) { + jQuery( this ).toggleClass( + value.call( this, i, getClass( this ), stateVal ), + stateVal + ); + } ); + } + + return this.each( function() { + var className, i, self, classNames; + + if ( isValidValue ) { + + // Toggle individual class names + i = 0; + self = jQuery( this ); + classNames = classesToArray( value ); + + while ( ( className = classNames[ i++ ] ) ) { + + // Check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( value === undefined || type === "boolean" ) { + className = getClass( this ); + if ( className ) { + + // Store className if set + dataPriv.set( this, "__className__", className ); + } + + // If the element has a class name or if we're passed `false`, + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + if ( this.setAttribute ) { + this.setAttribute( "class", + className || value === false ? + "" : + dataPriv.get( this, "__className__" ) || "" + ); + } + } + } ); + }, + + hasClass: function( selector ) { + var className, elem, + i = 0; + + className = " " + selector + " "; + while ( ( elem = this[ i++ ] ) ) { + if ( elem.nodeType === 1 && + ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { + return true; + } + } + + return false; + } +} ); + + + + +var rreturn = /\r/g; + +jQuery.fn.extend( { + val: function( value ) { + var hooks, ret, valueIsFunction, + elem = this[ 0 ]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || + jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && + "get" in hooks && + ( ret = hooks.get( elem, "value" ) ) !== undefined + ) { + return ret; + } + + ret = elem.value; + + // Handle most common string cases + if ( typeof ret === "string" ) { + return ret.replace( rreturn, "" ); + } + + // Handle cases where value is null/undef or number + return ret == null ? "" : ret; + } + + return; + } + + valueIsFunction = isFunction( value ); + + return this.each( function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( valueIsFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + + } else if ( typeof val === "number" ) { + val += ""; + + } else if ( Array.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + } ); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + } ); + } +} ); + +jQuery.extend( { + valHooks: { + option: { + get: function( elem ) { + + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + + // Support: IE <=10 - 11 only + // option.text throws exceptions (#14686, #14858) + // Strip and collapse whitespace + // https://html.spec.whatwg.org/#strip-and-collapse-whitespace + stripAndCollapse( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, i, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one", + values = one ? null : [], + max = one ? index + 1 : options.length; + + if ( index < 0 ) { + i = max; + + } else { + i = one ? index : 0; + } + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // Support: IE <=9 only + // IE8-9 doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + + // Don't return options that are disabled or in a disabled optgroup + !option.disabled && + ( !option.parentNode.disabled || + !nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + /* eslint-disable no-cond-assign */ + + if ( option.selected = + jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 + ) { + optionSet = true; + } + + /* eslint-enable no-cond-assign */ + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + return values; + } + } + } +} ); + +// Radios and checkboxes getter/setter +jQuery.each( [ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( Array.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + return elem.getAttribute( "value" ) === null ? "on" : elem.value; + }; + } +} ); + + + + +// Return jQuery for attributes-only inclusion + + +support.focusin = "onfocusin" in window; + + +var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, + stopPropagationCallback = function( e ) { + e.stopPropagation(); + }; + +jQuery.extend( jQuery.event, { + + trigger: function( event, data, elem, onlyHandlers ) { + + var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; + + cur = lastElement = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf( "." ) > -1 ) { + + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split( "." ); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf( ":" ) < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join( "." ); + event.rnamespace = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === ( elem.ownerDocument || document ) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { + lastElement = cur; + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] && + dataPriv.get( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( ( !special._default || + special._default.apply( eventPath.pop(), data ) === false ) && + acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name as the event. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + + if ( event.isPropagationStopped() ) { + lastElement.addEventListener( type, stopPropagationCallback ); + } + + elem[ type ](); + + if ( event.isPropagationStopped() ) { + lastElement.removeEventListener( type, stopPropagationCallback ); + } + + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + // Piggyback on a donor event to simulate a different one + // Used only for `focus(in | out)` events + simulate: function( type, elem, event ) { + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true + } + ); + + jQuery.event.trigger( e, null, elem ); + } + +} ); + +jQuery.fn.extend( { + + trigger: function( type, data ) { + return this.each( function() { + jQuery.event.trigger( type, data, this ); + } ); + }, + triggerHandler: function( type, data ) { + var elem = this[ 0 ]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +} ); + + +// Support: Firefox <=44 +// Firefox doesn't have focus(in | out) events +// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 +// +// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 +// focus(in | out) events fire after focus & blur events, +// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order +// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 +if ( !support.focusin ) { + jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + + // Handle: regular nodes (via `this.ownerDocument`), window + // (via `this.document`) & document (via `this`). + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + dataPriv.remove( doc, fix ); + + } else { + dataPriv.access( doc, fix, attaches ); + } + } + }; + } ); +} +var location = window.location; + +var nonce = { guid: Date.now() }; + +var rquery = ( /\?/ ); + + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml, parserErrorElem; + if ( !data || typeof data !== "string" ) { + return null; + } + + // Support: IE 9 - 11 only + // IE throws on parseFromString with invalid input. + try { + xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); + } catch ( e ) {} + + parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ]; + if ( !xml || parserErrorElem ) { + jQuery.error( "Invalid XML: " + ( + parserErrorElem ? + jQuery.map( parserErrorElem.childNodes, function( el ) { + return el.textContent; + } ).join( "\n" ) : + data + ) ); + } + return xml; +}; + + +var + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( Array.isArray( obj ) ) { + + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + + // Item is non-scalar (array or object), encode its numeric index. + buildParams( + prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", + v, + traditional, + add + ); + } + } ); + + } else if ( !traditional && toType( obj ) === "object" ) { + + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, valueOrFunction ) { + + // If value is a function, invoke it and use its return value + var value = isFunction( valueOrFunction ) ? + valueOrFunction() : + valueOrFunction; + + s[ s.length ] = encodeURIComponent( key ) + "=" + + encodeURIComponent( value == null ? "" : value ); + }; + + if ( a == null ) { + return ""; + } + + // If an array was passed in, assume that it is an array of form elements. + if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + } ); + + } else { + + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ); +}; + +jQuery.fn.extend( { + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map( function() { + + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + } ).filter( function() { + var type = this.type; + + // Use .is( ":disabled" ) so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + } ).map( function( _i, elem ) { + var val = jQuery( this ).val(); + + if ( val == null ) { + return null; + } + + if ( Array.isArray( val ) ) { + return jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ); + } + + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ).get(); + } +} ); + + +var + r20 = /%20/g, + rhash = /#.*$/, + rantiCache = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, + + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat( "*" ), + + // Anchor tag for parsing the document origin + originAnchor = document.createElement( "a" ); + +originAnchor.href = location.href; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; + + if ( isFunction( func ) ) { + + // For each dataType in the dataTypeExpression + while ( ( dataType = dataTypes[ i++ ] ) ) { + + // Prepend if requested + if ( dataType[ 0 ] === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); + + // Otherwise append + } else { + ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && + !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + } ); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var key, deep, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + + var ct, type, finalDataType, firstDataType, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s.throws ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { + state: "parsererror", + error: conv ? e : "No conversion from " + prev + " to " + current + }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend( { + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: location.href, + type: "GET", + isLocal: rlocalProtocol.test( location.protocol ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /\bxml\b/, + html: /\bhtml/, + json: /\bjson\b/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": JSON.parse, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var transport, + + // URL without anti-cache param + cacheURL, + + // Response headers + responseHeadersString, + responseHeaders, + + // timeout handle + timeoutTimer, + + // Url cleanup var + urlAnchor, + + // Request state (becomes false upon send and true upon completion) + completed, + + // To know if global events are to be dispatched + fireGlobals, + + // Loop variable + i, + + // uncached part of the url + uncached, + + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + + // Callbacks context + callbackContext = s.context || s, + + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && + ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks( "once memory" ), + + // Status-dependent callbacks + statusCode = s.statusCode || {}, + + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + + // Default abort message + strAbort = "canceled", + + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( completed ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( ( match = rheaders.exec( responseHeadersString ) ) ) { + responseHeaders[ match[ 1 ].toLowerCase() + " " ] = + ( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] ) + .concat( match[ 2 ] ); + } + } + match = responseHeaders[ key.toLowerCase() + " " ]; + } + return match == null ? null : match.join( ", " ); + }, + + // Raw string + getAllResponseHeaders: function() { + return completed ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + if ( completed == null ) { + name = requestHeadersNames[ name.toLowerCase() ] = + requestHeadersNames[ name.toLowerCase() ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( completed == null ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( completed ) { + + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } else { + + // Lazy-add the new callbacks in a way that preserves old ones + for ( code in map ) { + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ); + + // Add protocol if not provided (prefilters might expect it) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || location.href ) + "" ) + .replace( rprotocol, location.protocol + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; + + // A cross-domain request is in order when the origin doesn't match the current origin. + if ( s.crossDomain == null ) { + urlAnchor = document.createElement( "a" ); + + // Support: IE <=8 - 11, Edge 12 - 15 + // IE throws exception on accessing the href property if url is malformed, + // e.g. http://example.com:80x/ + try { + urlAnchor.href = s.url; + + // Support: IE <=8 - 11 only + // Anchor's host property isn't correctly set when s.url is relative + urlAnchor.href = urlAnchor.href; + s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== + urlAnchor.protocol + "//" + urlAnchor.host; + } catch ( e ) { + + // If there is an error parsing the URL, assume it is crossDomain, + // it can be rejected by the transport if it is invalid + s.crossDomain = true; + } + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( completed ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger( "ajaxStart" ); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + // Remove hash to simplify url manipulation + cacheURL = s.url.replace( rhash, "" ); + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // Remember the hash so we can put it back + uncached = s.url.slice( cacheURL.length ); + + // If data is available and should be processed, append data to url + if ( s.data && ( s.processData || typeof s.data === "string" ) ) { + cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; + + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add or update anti-cache param if needed + if ( s.cache === false ) { + cacheURL = cacheURL.replace( rantiCache, "$1" ); + uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) + + uncached; + } + + // Put hash and anti-cache on the URL that will be requested (gh-1732) + s.url = cacheURL + uncached; + + // Change '%20' to '+' if this is encoded form body content (gh-2658) + } else if ( s.data && s.processData && + ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { + s.data = s.data.replace( r20, "+" ); + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? + s.accepts[ s.dataTypes[ 0 ] ] + + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && + ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { + + // Abort if not done already and return + return jqXHR.abort(); + } + + // Aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + completeDeferred.add( s.complete ); + jqXHR.done( s.success ); + jqXHR.fail( s.error ); + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + + // If request was aborted inside ajaxSend, stop there + if ( completed ) { + return jqXHR; + } + + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = window.setTimeout( function() { + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + completed = false; + transport.send( requestHeaders, done ); + } catch ( e ) { + + // Rethrow post-completion exceptions + if ( completed ) { + throw e; + } + + // Propagate others as results + done( -1, e ); + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Ignore repeat invocations + if ( completed ) { + return; + } + + completed = true; + + // Clear timeout if it exists + if ( timeoutTimer ) { + window.clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Use a noop converter for missing script but not if jsonp + if ( !isSuccess && + jQuery.inArray( "script", s.dataTypes ) > -1 && + jQuery.inArray( "json", s.dataTypes ) < 0 ) { + s.converters[ "text script" ] = function() {}; + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader( "Last-Modified" ); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader( "etag" ); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + + // Extract error from statusText and normalize for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger( "ajaxStop" ); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +} ); + +jQuery.each( [ "get", "post" ], function( _i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + + // Shift arguments if data argument was omitted + if ( isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + // The url can be an options object (which then must have .url) + return jQuery.ajax( jQuery.extend( { + url: url, + type: method, + dataType: type, + data: data, + success: callback + }, jQuery.isPlainObject( url ) && url ) ); + }; +} ); + +jQuery.ajaxPrefilter( function( s ) { + var i; + for ( i in s.headers ) { + if ( i.toLowerCase() === "content-type" ) { + s.contentType = s.headers[ i ] || ""; + } + } +} ); + + +jQuery._evalUrl = function( url, options, doc ) { + return jQuery.ajax( { + url: url, + + // Make this explicit, since user can override this through ajaxSetup (#11264) + type: "GET", + dataType: "script", + cache: true, + async: false, + global: false, + + // Only evaluate the response if it is successful (gh-4126) + // dataFilter is not invoked for failure responses, so using it instead + // of the default converter is kludgy but it works. + converters: { + "text script": function() {} + }, + dataFilter: function( response ) { + jQuery.globalEval( response, options, doc ); + } + } ); +}; + + +jQuery.fn.extend( { + wrapAll: function( html ) { + var wrap; + + if ( this[ 0 ] ) { + if ( isFunction( html ) ) { + html = html.call( this[ 0 ] ); + } + + // The elements to wrap the target around + wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); + + if ( this[ 0 ].parentNode ) { + wrap.insertBefore( this[ 0 ] ); + } + + wrap.map( function() { + var elem = this; + + while ( elem.firstElementChild ) { + elem = elem.firstElementChild; + } + + return elem; + } ).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( isFunction( html ) ) { + return this.each( function( i ) { + jQuery( this ).wrapInner( html.call( this, i ) ); + } ); + } + + return this.each( function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + } ); + }, + + wrap: function( html ) { + var htmlIsFunction = isFunction( html ); + + return this.each( function( i ) { + jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html ); + } ); + }, + + unwrap: function( selector ) { + this.parent( selector ).not( "body" ).each( function() { + jQuery( this ).replaceWith( this.childNodes ); + } ); + return this; + } +} ); + + +jQuery.expr.pseudos.hidden = function( elem ) { + return !jQuery.expr.pseudos.visible( elem ); +}; +jQuery.expr.pseudos.visible = function( elem ) { + return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); +}; + + + + +jQuery.ajaxSettings.xhr = function() { + try { + return new window.XMLHttpRequest(); + } catch ( e ) {} +}; + +var xhrSuccessStatus = { + + // File protocol always yields status code 0, assume 200 + 0: 200, + + // Support: IE <=9 only + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrSupported = jQuery.ajaxSettings.xhr(); + +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +support.ajax = xhrSupported = !!xhrSupported; + +jQuery.ajaxTransport( function( options ) { + var callback, errorCallback; + + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(); + + xhr.open( + options.type, + options.url, + options.async, + options.username, + options.password + ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + callback = errorCallback = xhr.onload = + xhr.onerror = xhr.onabort = xhr.ontimeout = + xhr.onreadystatechange = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + + // Support: IE <=9 only + // On a manual native abort, IE9 throws + // errors on any property access that is not readyState + if ( typeof xhr.status !== "number" ) { + complete( 0, "error" ); + } else { + complete( + + // File: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } + } else { + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + + // Support: IE <=9 only + // IE9 has no XHR2 but throws on binary (trac-11426) + // For XHR2 non-text, let the caller handle it (gh-2498) + ( xhr.responseType || "text" ) !== "text" || + typeof xhr.responseText !== "string" ? + { binary: xhr.response } : + { text: xhr.responseText }, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" ); + + // Support: IE 9 only + // Use onreadystatechange to replace onabort + // to handle uncaught aborts + if ( xhr.onabort !== undefined ) { + xhr.onabort = errorCallback; + } else { + xhr.onreadystatechange = function() { + + // Check readyState before timeout as it changes + if ( xhr.readyState === 4 ) { + + // Allow onerror to be called first, + // but that will not handle a native abort + // Also, save errorCallback to a variable + // as xhr.onerror cannot be accessed + window.setTimeout( function() { + if ( callback ) { + errorCallback(); + } + } ); + } + }; + } + + // Create the abort callback + callback = callback( "abort" ); + + try { + + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) +jQuery.ajaxPrefilter( function( s ) { + if ( s.crossDomain ) { + s.contents.script = false; + } +} ); + +// Install script dataType +jQuery.ajaxSetup( { + accepts: { + script: "text/javascript, application/javascript, " + + "application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /\b(?:java|ecma)script\b/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +} ); + +// Handle cache's special case and crossDomain +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + } +} ); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function( s ) { + + // This transport only deals with cross domain or forced-by-attrs requests + if ( s.crossDomain || s.scriptAttrs ) { + var script, callback; + return { + send: function( _, complete ) { + script = jQuery( " + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 20 min exercises

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+Python environment +
+

From xkcd.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Exercises

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/environments/index.html b/branch/citation/environments/index.html new file mode 100644 index 0000000..5416238 --- /dev/null +++ b/branch/citation/environments/index.html @@ -0,0 +1,410 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 20 min exercise

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file,

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/exercises/index.html b/branch/citation/exercises/index.html new file mode 100644 index 0000000..950b754 --- /dev/null +++ b/branch/citation/exercises/index.html @@ -0,0 +1,679 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording dependencies

+

In dependencies.md:

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

Dependencies-2: Create a time-capsule for the future

+

Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording computational steps

+

In workflow-management.md:

+
+

Workflow-1: Scripted solution for processing 4 books

+

Somebody wrote a script (script.sh) to process all 4 books:

+
#!/usr/bin/env bash
+
+# loop over all books
+for title in abyss isles last sierra; do
+    python statistics/count.py data/${title}.txt > statistics/${title}.data
+    python plot/plot.py --data-file statistics/${title}.data --plot-file plot/${title}.png
+done
+
+
+

We can run it with:

+
$ bash script.sh
+
+
+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    • +
+ +
+

In workflow-management.md:

+
+

Workflow-2: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution +and the interesting file here is the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='statistics/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    conda: 'environment.yml'
+    log: 'statistics/{file}.log'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='plot/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    conda: 'environment.yml'
+    log: 'plot/{file}.log'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+

Snakemake uses declarative style: we describe dependencies but we let +Snakemake figure out the series of steps to produce results (targets). +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Exercise goals:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Sharing code and data

+

In sharing.md:

+
+

Sharing-1: Get a DOI from Zenodo

+

Digital object identifiers (DOI) are the backbone of the academic +reference and metrics system. In this exercise we will see how to +make a GitHub repository citable by archiving it on the +Zenodo archiving service. Zenodo is a +general-purpose open access repository created by OpenAIRE and CERN.

+
    +

  1. Sign in to Zenodo using your GitHub account. For this exercise, use the +sandbox service: https://sandbox.zenodo.org/login/. This is a test version of the real Zenodo platform.

    2. +

  2. Go to https://sandbox.zenodo.org/account/settings/github/.

    3. +

  3. Find the repository you wish to publish, +and flip the switch to ON.

    4. +

  4. Go to GitHub and create a release by clicking the Create a new release on the +right-hand side (a release is based on a Git tag, but is a higher-level GitHub feature). +You will need to enter a tag name (e.g. v0.1) in the “Choose a tag” box.

    5. +

  5. Creating a new release will trigger Zenodo into archiving your repository, +and a DOI badge will be displayed next to your repository after a minute +or two. You can include it in your GitHub README file: click the +DOI badge and copy the relevant format (Markdown, RST, HTML).

    6. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/genindex/index.html b/branch/citation/genindex/index.html new file mode 100644 index 0000000..34bf32b --- /dev/null +++ b/branch/citation/genindex/index.html @@ -0,0 +1,139 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/guide/index.html b/branch/citation/guide/index.html new file mode 100644 index 0000000..e155d12 --- /dev/null +++ b/branch/citation/guide/index.html @@ -0,0 +1,302 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

This was the schedule at our last workshop:

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Many participants do not share data or code, and in particular they are often +unaware that research output other than published articles can be assigned +digital object identifiers (DOIs). +The “Sharing code and data” is meant to bring awareness about FAIRness and Open Science +and to show how DOIs can be obtained for Git repositories..

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+

Perhaps we shouldn’t have done the Zenodo example - we could do a +quick demo, but because of limited time, I’m not sure if it conveyed +how cool it was. Maybe we should have simply said it. Alternatively, +we could have not done the Docker demonstration and given more time +for Zenodo.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/index.html b/branch/citation/index.html new file mode 100644 index 0000000..fae8c0f --- /dev/null +++ b/branch/citation/index.html @@ -0,0 +1,192 @@ + + + + + + + Reproducible research — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • be able to apply well organized directory structure for their project

    • +

  • remember the FAIR principles

    • +

  • understand that code can have dependencies, and know how to document them

    • +

  • if a computational studies contains several steps, be able to document them

    • +

  • know about use cases for containers

    • +

  • knowing the pros and cons of manual documentation vs. scripted automation vs. workflow management

    • +

  • be able to create a DOI for research output like code or data

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/motivation/index.html b/branch/citation/motivation/index.html new file mode 100644 index 0000000..a99a11d --- /dev/null +++ b/branch/citation/motivation/index.html @@ -0,0 +1,211 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[citation needed]

+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs - figure by Heidi Seibold, CC-BY 4.0 +
+

[Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/objects.inv b/branch/citation/objects.inv new file mode 100644 index 0000000..11cee94 --- /dev/null +++ b/branch/citation/objects.inv @@ -0,0 +1,7 @@ +# Sphinx inventory version 2 +# Project: Reproducible research +# Version: +# The remainder of this file is compressed using zlib. +x}Mn bfkn{J' 0imp ]a}oA-zP=ɸOƺ2](99xC֗cP›!Qqm2mTk:D=Xy $t z-1idmO-Gź;3vdvZ -s؎`A6oA\+gqU,aaUD韰141[y43 _vT5 +(Ns u)ޕr +J\-]N!ܽ#KSaZj{/~ƞ \ No newline at end of file diff --git a/branch/citation/organizing-projects/index.html b/branch/citation/organizing-projects/index.html new file mode 100644 index 0000000..fd5b64c --- /dev/null +++ b/branch/citation/organizing-projects/index.html @@ -0,0 +1,297 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the most basic steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist:

    +
      +

    • Overleaf: an online, collaborative LaTeX editor (has Git integration)

      • +

    • Authorea: collaborative platform for preprints (apparently also has Git integration)

      • +

    • HackMD: an online collaborative Markdown editor (has Git integration)

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+
+
+

Discussion on reproducibility

+
+

Discuss in collaborative document or with your team members

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+

Discuss in collaborative document or with your team members

+
- What tools are you using when organizing your projects?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +

  • Reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/search/index.html b/branch/citation/search/index.html new file mode 100644 index 0000000..8675c31 --- /dev/null +++ b/branch/citation/search/index.html @@ -0,0 +1,153 @@ + + + + + + Search — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
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"Directory structure for projects": [[6, "directory-structure-for-projects"]], "Tracking source code, data, and results": [[6, "tracking-source-code-data-and-results"]], "Reproducible publications": [[6, "reproducible-publications"]], "Discussion on reproducibility": [[6, "discussion-on-reproducibility"]], "Keypoints": [[6, "keypoints-0"], [7, "keypoints-0"]], "Sharing research data": [[7, "sharing-research-data"]], "FAIR principles": [[7, "fair-principles"]], "Discuss open science": [[7, "discussion-0"]], "Exercise - Connecting repositories to Zenodo": [[7, "exercise-connecting-repositories-to-zenodo"]], "Services for sharing and collaborating on research data": [[7, "services-for-sharing-and-collaborating-on-research-data"]], "Resources for data management": [[7, "resources-for-data-management"]], "Further reading on reproducibility and open science": [[7, "further-reading-on-reproducibility-and-open-science"]], "Several steps from input data to result": [[8, "several-steps-from-input-data-to-result"]], "Discussion": [[8, "discussion-0"]], "Exercise": [[8, "exercise"]], "Exercise preparation": [[8, "prerequisites-0"]], "Why Snakemake?": [[8, "why-snakemake"]], "Similar tools": [[8, "similar-tools"]], "Visualizing the workflow": [[8, "visualizing-the-workflow"]]}, "indexentries": {}}) \ No newline at end of file diff --git a/branch/citation/sharing/index.html b/branch/citation/sharing/index.html new file mode 100644 index 0000000..009392f --- /dev/null +++ b/branch/citation/sharing/index.html @@ -0,0 +1,361 @@ + + + + + + + Sharing code and data — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Sharing code and data

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Questions

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  • How can I share research code and data?

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Objectives

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  • Discuss the pros and cons of open science

    • +

  • Learn how to mint a DOI for your project

    • +
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Instructor note

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  • 10 min teaching

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  • 15 min exercises

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Sharing research data

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The Open Science movement encourages researchers +to share research output beyond the contents of a +published academic article (and possibly supplementary information).

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+Research comic +
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Arguments in favor (from Wikipedia):

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  • Open access publication of research reports and data allows for rigorous peer-review

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  • Science is publicly funded so all results of the research should be publicly available

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  • Open Science will make science more reproducible and transparent

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  • Open Science has more impact

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  • Open Science will help answer uniquely complex questions

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Arguments against (from Wikipedia):

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    +

  • Too much unsorted information overwhelms scientists

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  • Potential misuse

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  • The public will misunderstand science data

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  • Increasing the scale of science will make verification of any discovery more difficult

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  • Low-quality science

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+Research comic +
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(This image was created by Scriberia for The +Turing Way community and is used under a +CC-BY licence. The image was obtained from https://zenodo.org/record/3332808.)

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FAIR principles

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+Research comic +
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(This image was created by Scriberia for The +Turing Way community and is used under a +CC-BY licence. The image was obtained from https://zenodo.org/record/3332808.)

+

“FAIR” is the current buzzword for data management. You may be asked +about it in, for example, making data management plans for grants:

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  • Findable

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    • Will anyone else know that your data exists?

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    • Solutions: put it in a standard repository, or at least a +description of the data. Get a digital object identifier (DOI).

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  • Accessible

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    • Once someone knows that the data exists, can they get it?

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    • Usually solved by being in a repository, but for non-open data, +may require more procedures.

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  • Interoperable

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    • Is your data in a format that can be used by others, like csv +instead of PDF?

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    • Or better than csv. Example: 5-star open data

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  • Reusable

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    • Is there a license allowing others to re-use?

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Even though this is usually referred to as “open data”, it means +considering and making good decisions, even if non-open.

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FAIR principles are usually discussed in the context of data, +but they apply also for research software.

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Note that FAIR principles do not require data/software to be open.

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Discuss open science

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  • Do you share any other research outputs besides published articles and possibly source code?

    • +

  • Discuss pros and cons of sharing research data.

    • +
+
+
+
+
+

Exercise - Connecting repositories to Zenodo

+
+

Sharing-1: Get a DOI from Zenodo

+

Digital object identifiers (DOI) are the backbone of the academic +reference and metrics system. In this exercise we will see how to +make a GitHub repository citable by archiving it on the +Zenodo archiving service. Zenodo is a +general-purpose open access repository created by OpenAIRE and CERN.

+
    +

  1. Sign in to Zenodo using your GitHub account. For this exercise, use the +sandbox service: https://sandbox.zenodo.org/login/. This is a test version of the real Zenodo platform.

    2. +

  2. Go to https://sandbox.zenodo.org/account/settings/github/.

    3. +

  3. Find the repository you wish to publish, +and flip the switch to ON.

    4. +

  4. Go to GitHub and create a release by clicking the Create a new release on the +right-hand side (a release is based on a Git tag, but is a higher-level GitHub feature). +You will need to enter a tag name (e.g. v0.1) in the “Choose a tag” box.

    5. +

  5. Creating a new release will trigger Zenodo into archiving your repository, +and a DOI badge will be displayed next to your repository after a minute +or two. You can include it in your GitHub README file: click the +DOI badge and copy the relevant format (Markdown, RST, HTML).

    6. +
+
+
+
+
+

Services for sharing and collaborating on research data

+

To find a research data repository for your data, you can search on the +Registry of Research Data Repositories (re3data) +platform and filter by country, content type, discipline, etc.

+

International:

+
    +

  • Zenodo: A general-purpose open access repository +created by OpenAIRE and CERN. Integration with GitHub, allows +researchers to upload files up to 50 GB.

    • +

  • Figshare: Online digital repository where researchers +can preserve and share their research outputs (figures, datasets, images and videos). +Users can make all of their research outputs available in a citable, +shareable and discoverable manner.

    • +

  • EUDAT: European platform for researchers and practitioners from any research discipline to preserve, find, access, and process data in a trusted environment.

    • +

  • Dryad: A general-purpose home for a wide diversity of datatypes, +governed by a nonprofit membership organization. +A curated resource that makes the data underlying scientific publications discoverable, +freely reusable, and citable.

    • +

  • The Open Science Framework: Gives free accounts for collaboration +around files and other research artifacts. Each account can have up to 5 GB of files +without any problem, and it remains private until you make it public.

    • +
+

Sweden:

+ +

Norway:

+ +

Denmark:

+ +

Finland:

+ +
+
+
+

Resources for data management

+ +
+
+
+

Further reading on reproducibility and open science

+ +
+

Keypoints

+
    +

  • Consider sharing other research outputs than articles.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/citation/workflow-management/index.html b/branch/citation/workflow-management/index.html new file mode 100644 index 0000000..35b21f5 --- /dev/null +++ b/branch/citation/workflow-management/index.html @@ -0,0 +1,393 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 20 min exercises

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+
+

Discussion

+

We have two steps and 4 books. But imagine having 4 steps and processing 500 books. +Can you relate? Are you using similar setups in your research? How do you record them?

+
+
+

Kitchen analogy

+
+Busy kitchen +
+

Now we have many similar meals to prepare and possibly many chefs +present (cores) and workflow tools can help us to plan and document the steps +and run them efficiently. [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

Exercise

+
+

Exercise preparation

+

The exercise (below) and pre-exercise discussion uses a simple +word-count repository +(https://github.com/coderefinery/word-count). We should clone the +repository already to prepare to work on it.

+

You could do the exercise either on your own computer, or the Binder +cloud service:

+

On your own computer:

+
    +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Scripted solution for processing 4 books

+

Somebody wrote a script (script.sh) to process all 4 books:

+
#!/usr/bin/env bash
+
+# loop over all books
+for title in abyss isles last sierra; do
+    python statistics/count.py data/${title}.txt > statistics/${title}.data
+    python plot/plot.py --data-file statistics/${title}.data --plot-file plot/${title}.png
+done
+
+
+

We can run it with:

+
$ bash script.sh
+
+
+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    • +
+ +
+
+

Workflow-2: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution +and the interesting file here is the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='statistics/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    conda: 'environment.yml'
+    log: 'statistics/{file}.log'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='plot/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    conda: 'environment.yml'
+    log: 'plot/{file}.log'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+

Snakemake uses declarative style: we describe dependencies but we let +Snakemake figure out the series of steps to produce results (targets). +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Exercise goals:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all HPC schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Is is possible to define isolated software environments per rule, see here.

    • +

  • Also possible to run workflows in Docker or Apptainer containers.

    • +

  • Workflows can be pushed out to run on a cluster or in the cloud without modifications to scale up.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+
+
+

Similar tools

+ +
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz). It’s not necessary to +run this step yourself.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/.buildinfo b/branch/enrico-dependencies/.buildinfo new file mode 100644 index 0000000..94714cf --- /dev/null +++ b/branch/enrico-dependencies/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 639eb01f9a14f2c0189bf299fb057e86 +tags: d77d1c0d9ca2f4c8421862c7c5a0d620 diff --git a/branch/enrico-dependencies/.nojekyll b/branch/enrico-dependencies/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/branch/enrico-dependencies/_images/arrows.png b/branch/enrico-dependencies/_images/arrows.png new file mode 100644 index 0000000..2aa4a80 Binary files /dev/null and b/branch/enrico-dependencies/_images/arrows.png differ diff --git a/branch/enrico-dependencies/_images/dependency.png b/branch/enrico-dependencies/_images/dependency.png new file mode 100644 index 0000000..e07722d Binary files /dev/null and b/branch/enrico-dependencies/_images/dependency.png differ diff --git a/branch/enrico-dependencies/_images/docker_meme.jpg b/branch/enrico-dependencies/_images/docker_meme.jpg new file mode 100644 index 0000000..78d1b11 Binary files /dev/null and b/branch/enrico-dependencies/_images/docker_meme.jpg differ diff --git a/branch/enrico-dependencies/_images/libraries.png b/branch/enrico-dependencies/_images/libraries.png new file mode 100644 index 0000000..44202e3 Binary files /dev/null and b/branch/enrico-dependencies/_images/libraries.png differ diff --git a/branch/enrico-dependencies/_images/linux.png b/branch/enrico-dependencies/_images/linux.png new file mode 100644 index 0000000..1877b94 Binary files /dev/null and b/branch/enrico-dependencies/_images/linux.png differ diff --git a/branch/enrico-dependencies/_images/macos.png b/branch/enrico-dependencies/_images/macos.png new file mode 100644 index 0000000..3054c58 Binary files /dev/null and b/branch/enrico-dependencies/_images/macos.png differ diff --git a/branch/enrico-dependencies/_images/recipe.png b/branch/enrico-dependencies/_images/recipe.png new file mode 100644 index 0000000..1d6bd54 Binary files /dev/null and b/branch/enrico-dependencies/_images/recipe.png differ diff --git a/branch/enrico-dependencies/_images/repro-pyramid.png b/branch/enrico-dependencies/_images/repro-pyramid.png new file mode 100644 index 0000000..a8aec07 Binary files /dev/null and b/branch/enrico-dependencies/_images/repro-pyramid.png differ diff --git a/branch/enrico-dependencies/_images/reproducibility_nature.jpg b/branch/enrico-dependencies/_images/reproducibility_nature.jpg new file mode 100644 index 0000000..7967116 Binary files /dev/null and b/branch/enrico-dependencies/_images/reproducibility_nature.jpg differ diff --git a/branch/enrico-dependencies/_images/reproducible_research_plus_lessons.png b/branch/enrico-dependencies/_images/reproducible_research_plus_lessons.png new file mode 100644 index 0000000..fd092a6 Binary files /dev/null and b/branch/enrico-dependencies/_images/reproducible_research_plus_lessons.png differ diff --git a/branch/enrico-dependencies/_images/research_comic_phd.gif b/branch/enrico-dependencies/_images/research_comic_phd.gif new file mode 100644 index 0000000..f9be5a2 Binary files /dev/null and b/branch/enrico-dependencies/_images/research_comic_phd.gif differ diff --git a/branch/enrico-dependencies/_images/snakemake.png b/branch/enrico-dependencies/_images/snakemake.png new file mode 100644 index 0000000..ebe4f9e Binary files /dev/null and b/branch/enrico-dependencies/_images/snakemake.png differ diff --git a/branch/enrico-dependencies/_images/snakemake_dag.png b/branch/enrico-dependencies/_images/snakemake_dag.png new file mode 100644 index 0000000..eb4ae4e Binary files /dev/null and b/branch/enrico-dependencies/_images/snakemake_dag.png differ diff --git a/branch/enrico-dependencies/_images/windows.png b/branch/enrico-dependencies/_images/windows.png new file mode 100644 index 0000000..45d2668 Binary files /dev/null and b/branch/enrico-dependencies/_images/windows.png differ diff --git a/branch/enrico-dependencies/_sources/dependencies.md.txt b/branch/enrico-dependencies/_sources/dependencies.md.txt new file mode 100644 index 0000000..5a93101 --- /dev/null +++ b/branch/enrico-dependencies/_sources/dependencies.md.txt @@ -0,0 +1,359 @@ +# Recording dependencies + +```{questions} +- How can we communicate different versions of software dependencies? +``` + +```{instructor-note} +- 10 min teaching +- 10 min demo +``` + +Our codes often depend on other codes that in turn depend on other codes ... + +- **Reproducibility**: We can version-control our code with Git but how should we version-control dependencies? + How can we capture and communicate dependencies? +- **Dependency hell**: Different codes on the same environment can have conflicting dependencies. + +```{figure} img/dependency.png +:alt: An image showing blocks (=codes) depending on each other for stability +:width: 60% + +From [xkcd - dependency](https://xkcd.com/2347/). Another image that might be familiar to some of you working with Python can be found on [xkcd - superfund](https://xkcd.com/1987/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Demo + +``````{challenge} Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +Answer in the collaborative document: + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} Dependencies-2: Create a time-capsule for the future +Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + We start from an existing conda environment. Try this either with your own project or inside the "coderefinery" conda + environment. For demonstration puprposes, you can also create an environment with: + + ```console + $ conda env create -f myenv.yml + ``` + Where the file `myenv.yml` could have some python libraries with unspecified versions: + + ``` + name: myenv + channels: + - conda-forge + - defaults + dependencies: + - python=3.10 + - numpy + - pandas + - seaborn + ``` + + After creating the environment we can activate it with + + ``` + conda activate myenv + ``` + + Now we can freeze the environment into a new YAML file with: + + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In the future — or on a different computer — we can re-create this environment with: + + ```console + $ conda env create -f environment.yml + ``` + + What happens instead when you run the following command? + + ```console + $ conda env export --from-history > environment_fromhistory.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` + + +```{keypoints} +- Recording dependencies with versions can make it easier for the next person to execute your code +- There are many tools to record dependencies +``` diff --git a/branch/enrico-dependencies/_sources/environments.md.txt b/branch/enrico-dependencies/_sources/environments.md.txt new file mode 100644 index 0000000..e36045f --- /dev/null +++ b/branch/enrico-dependencies/_sources/environments.md.txt @@ -0,0 +1,286 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 10 min demo +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**. + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +## You may have use for containers in different ways + +- Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead! +- You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container! + - If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough. + +## The container recipe + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + +````{exercise} (optional) Containers-2: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` + +## Resources for further learning + +- [Carpentries incubator lesson on Docker](https://carpentries-incubator.github.io/docker-introduction/) +- [Carpentries incubator lesson on Singularity/Apptainer](https://carpentries-incubator.github.io/singularity-introduction/) + + +```{keypoints} +- Containers can be helpful if complex setups are needed to running a specific software +- They can also be helpful for prototyping without "messing up" your own computing environment, or for running software that requires a different operating system than your own +``` diff --git a/branch/enrico-dependencies/_sources/exercises.md.txt b/branch/enrico-dependencies/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/branch/enrico-dependencies/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/branch/enrico-dependencies/_sources/guide.md.txt b/branch/enrico-dependencies/_sources/guide.md.txt new file mode 100644 index 0000000..97261f0 --- /dev/null +++ b/branch/enrico-dependencies/_sources/guide.md.txt @@ -0,0 +1,155 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +Two example schedules for this lesson: + +This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Overview of CR and how it all fits together +- 09:10 - 09:20 Reproducible research, [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:27 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:27 - 09:35 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) - discussion +- 09:35 - 10:00 Snakemake exercise (25 min) +- 10:00 - 10:10 Break +- 10:10 - 10:15 Summary of workflows and the exercise +- 10:15 - 10:30 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- 10:30 - 10:40 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) +- 10:40 - 11:00 Container-1 exercise (20 min) +- 11:00 - 11.05 Wrapup + +This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break): + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + diff --git a/branch/enrico-dependencies/_sources/index.rst.txt b/branch/enrico-dependencies/_sources/index.rst.txt new file mode 100644 index 0000000..05828e6 --- /dev/null +++ b/branch/enrico-dependencies/_sources/index.rst.txt @@ -0,0 +1,57 @@ +.. _index: + +Reproducible research - Preparing code to be usable by you and others in the future +=================================================================================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves and others. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - Be able to apply well organized directory structure for their project + - Understand that code can have dependencies, and know how to document them + - Be able to document computational steps, and have an idea when it can be useful + - Know about use cases for containers + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + intro.md + motivation.md + organizing-projects.md + workflow-management.md + dependencies.md + environments.md + where-to-go.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/branch/enrico-dependencies/_sources/intro.md.txt b/branch/enrico-dependencies/_sources/intro.md.txt new file mode 100644 index 0000000..6690f38 --- /dev/null +++ b/branch/enrico-dependencies/_sources/intro.md.txt @@ -0,0 +1,16 @@ +# Introduction - How it all connects + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +--- + +```{figure} img/reproducible_research_plus_lessons.png +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, ] + diff --git a/branch/enrico-dependencies/_sources/motivation.md.txt b/branch/enrico-dependencies/_sources/motivation.md.txt new file mode 100644 index 0000000..07d1f8e --- /dev/null +++ b/branch/enrico-dependencies/_sources/motivation.md.txt @@ -0,0 +1,74 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[Steeves, Vicky (2017) in "Reproducibility Librarianship," Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4] + +This also means that you can think about it from the beginning of your research life cycle! + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` + +```{keypoints} +- Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch +``` \ No newline at end of file diff --git a/branch/enrico-dependencies/_sources/organizing-projects.md.txt b/branch/enrico-dependencies/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..c46ad19 --- /dev/null +++ b/branch/enrico-dependencies/_sources/organizing-projects.md.txt @@ -0,0 +1,120 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the first steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* Check the [Git-intro lesson](https://coderefinery.github.io/git-intro/) for a reminder. + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in the collaborative document: + +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on the fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +## Some tools and templates + +- [R devtools](https://devtools.r-lib.org/) +- [Python cookiecutter template](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) +- [Reproducible research template](https://github.com/the-turing-way/reproducible-project-template) by the Turing Way + +More tools and templates in [Heidi Seibolds blog](https://heidiseibold.ck.page/posts/setting-up-a-fair-and-reproducible-project). + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration: + - [Overleaf](https://www.overleaf.com) or [Typst](https://typst.app/): online, collaborative LaTeX editor + - [Authorea](https://www.authorea.com): collaborative platform for preprints + - [HackMD](https://hackmd.io/) or [HedgeDoc](https://hedgedoc.org/): online collaborative Markdown editors + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as, see also our [Jupyter lesson](https://coderefinery.github.io/jupyter/) later in this workshop. + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + +```{keypoints} +- An organized project directory structure helps with reproducibility. +``` diff --git a/branch/enrico-dependencies/_sources/where-to-go.md.txt b/branch/enrico-dependencies/_sources/where-to-go.md.txt new file mode 100644 index 0000000..b524992 --- /dev/null +++ b/branch/enrico-dependencies/_sources/where-to-go.md.txt @@ -0,0 +1,53 @@ +# Where to go from here + +```{objectives} +- Understand when tools discussed in this episode can be useful +``` + +```{instructor-note} +- 10 min teaching/discussion +``` + +This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project. + +## Important for every project + +* Clear file structure for your project +* At least consider the possibility that someone, maybe you may want to reproduce your work + * Can you do something (small) to make it easier? + * If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help. + +## Workflow tools will maybe make sense in the future + +* In many cases, it is probably not needed +* You will want to consider workflow tools: + * When processing many files with many steps + * Steps or files may change + * Your main script, connecting your steps gets very long + * ... + +## When should I worry about dependencies? + +* Your code depends on multiple other packages +* You want to avoid questions like: "What do I need to install to run your code" +* You want help yourself running your code + * After a few years + * On a different computer + * ... + +## Containers seem amazing, but do I have use for them? + +* Maybe not yet, but knowing that you can ... + * Run Linux tools on your Windows computer + * Run different versions of same software on your computer + * Follow the "easy installation instructions" for an operating system that is not your own + * Get a fully configured environment instead of only installing a tool + * Share your setup and configurations with others +... can be very beneficial :) + + +```{keypoints} +- Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution. +- Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/branch/enrico-dependencies/_sources/workflow-management.md.txt b/branch/enrico-dependencies/_sources/workflow-management.md.txt new file mode 100644 index 0000000..83caaf6 --- /dev/null +++ b/branch/enrico-dependencies/_sources/workflow-management.md.txt @@ -0,0 +1,241 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 5 min teaching +- 15 min demo +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: + +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps. + +Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But **imagine having 4 steps and 500 books**. +How could we deal with this? + +As a first idea we could express the workflow with a script. The repository includes such script called `run_all.sh`. + +We can run it with: + +```console +$ bash run_all.sh +``` + +This is **imperative style**: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another. + +````{discussion} +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + + ```{solution} + The advantage of this solution compared to processing one by one is more automation: We can generate all. + This is not only easier, it is also less error-prone. + + Yes, the scripted solution can be reproducible. But could you easily run it e.g. on a Windows computer? + + If we had more steps and once steps start to be time-consuming, a limitation of + a scripted solution is that it tries to run all steps always. Rerunning only + part of the steps or only part of the input data requires us to outcomment or change lines in our script in between runs which can again become tedious and error-prone. + ``` +```` + +--- + +## Workflow tools + +Sometimes it may be helpful to go from imperative to declarative style. Rather than saying "do this and then that" we describe dependencies but we let the tool figure out the series of steps to produce results. + +### Example workflow tool: [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) + +Snakemake (inspired by [GNU Make](https://www.gnu.org/software/make/)) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition. + +--- + +## A demo + +````{prereq} Preparation +The exercise (below) and pre-exercise discussion uses the +word-count repository +() which we need to clone to work on it. + +If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the [CodeRefinery installation instruction page](https://coderefinery.github.io/installation/)), or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Install the necessary tools +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution in the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='code/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='code/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' + +``` + +We can see that Snakemake uses **declarative style**: +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Steps: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containing "shell". +``` +```` + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle **learning curve**. +- Free, open-source, and **installs easily** via conda or pip. +- **Cross-platform** (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them **in parallel**. +- Is is possible to define **isolated software environments** per rule, e.g. by adding `conda: 'environment.yml'` to a rule. +- Also possible to run workflows in Docker or Apptainer **containers** e.g. by adding `container: 'docker://some-org/some-tool#2.3.1'` to a rule. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is **completely general**. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + +Tools like Snakemake help us with **reproducibility** by supporting us with **automation**, **scalability** and **portability** of our workflows. + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. +- [Book on building reproducible analytical pipelines with R](https://raps-with-r.dev/) + +```{keypoints} +- Computational steps can be recorded in many ways +- Workflow tools can help, if there are many steps to be executed +``` diff --git a/branch/enrico-dependencies/_static/_sphinx_javascript_frameworks_compat.js b/branch/enrico-dependencies/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/enrico-dependencies/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-dependencies/_static/check-solid.svg b/branch/enrico-dependencies/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/enrico-dependencies/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/enrico-dependencies/_static/clipboard.min.js b/branch/enrico-dependencies/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/enrico-dependencies/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/enrico-dependencies/_static/copybutton.css b/branch/enrico-dependencies/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/enrico-dependencies/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/enrico-dependencies/_static/copybutton.js b/branch/enrico-dependencies/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/enrico-dependencies/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/enrico-dependencies/_static/copybutton_funcs.js b/branch/enrico-dependencies/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/enrico-dependencies/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/enrico-dependencies/_static/css/badge_only.css b/branch/enrico-dependencies/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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+ if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); // readthedocs version selector + + // Add other formats here. +} + + +var slideshow = minipres; + +if (window.location.search.match(/[?&](minipres|slideshow|pres)([=&]|$)/) ) { + //minipres() + window.addEventListener("load", minipres); +} else if (window.location.search.match(/[?&](plain)([=&]|$)/) ) { + window.addEventListener("load", hide); +} diff --git a/branch/enrico-dependencies/_static/minus.png b/branch/enrico-dependencies/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/branch/enrico-dependencies/_static/minus.png differ diff --git a/branch/enrico-dependencies/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css b/branch/enrico-dependencies/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css new file mode 100644 index 0000000..3356631 --- /dev/null +++ b/branch/enrico-dependencies/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css @@ -0,0 +1,2342 @@ +/* Variables */ +:root { + --mystnb-source-bg-color: #f7f7f7; + --mystnb-stdout-bg-color: #fcfcfc; + --mystnb-stderr-bg-color: #fdd; + --mystnb-traceback-bg-color: #fcfcfc; + --mystnb-source-border-color: #ccc; + --mystnb-source-margin-color: green; + --mystnb-stdout-border-color: #f7f7f7; + --mystnb-stderr-border-color: #f7f7f7; + --mystnb-traceback-border-color: #ffd6d6; + --mystnb-hide-prompt-opacity: 70%; + --mystnb-source-border-radius: .4em; + --mystnb-source-border-width: 1px; +} + +/* Whole cell */ +div.container.cell { + padding-left: 0; + margin-bottom: 1em; +} + +/* Removing all background formatting so we can control at the div level */ +.cell_input div.highlight, +.cell_output pre, +.cell_input pre, +.cell_output .output { + border: none; + box-shadow: none; +} + +.cell_output .output pre, +.cell_input pre { + margin: 0px; +} + +/* Input cells */ +div.cell div.cell_input, +div.cell details.above-input>summary { + padding-left: 0em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; 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+ border: 1px solid var(--mystnb-traceback-border-color); +} + +/* Collapsible cell content */ +div.cell details.above-input div.cell_input { + border-top-left-radius: 0; + border-top-right-radius: 0; + border-top: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; +} + +div.cell div.cell_input.above-output-prompt { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; +} + +div.cell details.above-input>summary { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; + border-bottom: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; + padding-left: 1em; + margin-bottom: 0; +} + +div.cell details.above-output>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + 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.-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/enrico-dependencies/_static/plus.png b/branch/enrico-dependencies/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/enrico-dependencies/_static/plus.png differ diff --git a/branch/enrico-dependencies/_static/pygments.css b/branch/enrico-dependencies/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/enrico-dependencies/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; font-style: italic } /* 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Literal.Number.Bin */ +.highlight .mf { color: #666666 } /* Literal.Number.Float */ +.highlight .mh { color: #666666 } /* Literal.Number.Hex */ +.highlight .mi { color: #666666 } /* Literal.Number.Integer */ +.highlight .mo { color: #666666 } /* Literal.Number.Oct */ +.highlight .sa { color: #BA2121 } /* Literal.String.Affix */ +.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */ +.highlight .sc { color: #BA2121 } /* Literal.String.Char */ +.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */ +.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #BA2121 } /* Literal.String.Double */ +.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/enrico-dependencies/_static/searchtools.js b/branch/enrico-dependencies/_static/searchtools.js new file mode 100644 index 0000000..7918c3f --- /dev/null +++ b/branch/enrico-dependencies/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/enrico-dependencies/_static/sphinx_highlight.js b/branch/enrico-dependencies/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/enrico-dependencies/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/enrico-dependencies/_static/sphinx_lesson.css b/branch/enrico-dependencies/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/enrico-dependencies/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/enrico-dependencies/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/enrico-dependencies/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/enrico-dependencies/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/enrico-dependencies/_static/tabs.css b/branch/enrico-dependencies/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/enrico-dependencies/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/enrico-dependencies/_static/tabs.js b/branch/enrico-dependencies/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/enrico-dependencies/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/enrico-dependencies/_static/term_role_formatting.css b/branch/enrico-dependencies/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/enrico-dependencies/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/enrico-dependencies/_static/togglebutton.css b/branch/enrico-dependencies/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/enrico-dependencies/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-dependencies/_static/togglebutton.js b/branch/enrico-dependencies/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/enrico-dependencies/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/enrico-dependencies/dependencies/index.html b/branch/enrico-dependencies/dependencies/index.html new file mode 100644 index 0000000..a12ff32 --- /dev/null +++ b/branch/enrico-dependencies/dependencies/index.html @@ -0,0 +1,457 @@ + + + + + + + Recording dependencies — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

We start from an existing conda environment. Try this either with your own project or inside the “coderefinery” conda +environment. For demonstration puprposes, you can also create an environment with:

+
$ conda env create -f myenv.yml
+
+
+

Where the file myenv.yml could have some python libraries with unspecified versions:

+
name: myenv
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - numpy
+  - pandas
+  - seaborn
+
+
+

After creating the environment we can activate it with

+
conda activate myenv
+
+
+

Now we can freeze the environment into a new YAML file with:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In the future — or on a different computer — we can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

What happens instead when you run the following command?

+
$ conda env export --from-history > environment_fromhistory.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/environments/index.html b/branch/enrico-dependencies/environments/index.html new file mode 100644 index 0000000..b52ec23 --- /dev/null +++ b/branch/enrico-dependencies/environments/index.html @@ -0,0 +1,445 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/exercises/index.html b/branch/enrico-dependencies/exercises/index.html new file mode 100644 index 0000000..4083d2f --- /dev/null +++ b/branch/enrico-dependencies/exercises/index.html @@ -0,0 +1,653 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording computational steps

+

In workflow-management.md:

+ +

In workflow-management.md:

+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording dependencies

+

In dependencies.md:

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

We start from an existing conda environment. Try this either with your own project or inside the “coderefinery” conda +environment. For demonstration puprposes, you can also create an environment with:

+
$ conda env create -f myenv.yml
+
+
+

Where the file myenv.yml could have some python libraries with unspecified versions:

+
name: myenv
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - numpy
+  - pandas
+  - seaborn
+
+
+

After creating the environment we can activate it with

+
conda activate myenv
+
+
+

Now we can freeze the environment into a new YAML file with:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In the future — or on a different computer — we can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

What happens instead when you run the following command?

+
$ conda env export --from-history > environment_fromhistory.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/genindex/index.html b/branch/enrico-dependencies/genindex/index.html new file mode 100644 index 0000000..040ed0f --- /dev/null +++ b/branch/enrico-dependencies/genindex/index.html @@ -0,0 +1,143 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/guide/index.html b/branch/enrico-dependencies/guide/index.html new file mode 100644 index 0000000..3ba180b --- /dev/null +++ b/branch/enrico-dependencies/guide/index.html @@ -0,0 +1,312 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/index.html b/branch/enrico-dependencies/index.html new file mode 100644 index 0000000..4273472 --- /dev/null +++ b/branch/enrico-dependencies/index.html @@ -0,0 +1,194 @@ + + + + + + + Reproducible research - Preparing code to be usable by you and others in the future — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research - Preparing code to be usable by you and others in the future
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/intro/index.html b/branch/enrico-dependencies/intro/index.html new file mode 100644 index 0000000..14bc998 --- /dev/null +++ b/branch/enrico-dependencies/intro/index.html @@ -0,0 +1,157 @@ + + + + + + + Introduction - How it all connects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/lesson.pdf b/branch/enrico-dependencies/lesson.pdf new file mode 100644 index 0000000..b31cf46 Binary files /dev/null and b/branch/enrico-dependencies/lesson.pdf differ diff --git a/branch/enrico-dependencies/motivation/index.html b/branch/enrico-dependencies/motivation/index.html new file mode 100644 index 0000000..a1fee3f --- /dev/null +++ b/branch/enrico-dependencies/motivation/index.html @@ -0,0 +1,217 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/objects.inv b/branch/enrico-dependencies/objects.inv new file mode 100644 index 0000000..e482281 Binary files /dev/null and b/branch/enrico-dependencies/objects.inv differ diff --git a/branch/enrico-dependencies/organizing-projects/index.html b/branch/enrico-dependencies/organizing-projects/index.html new file mode 100644 index 0000000..3ba7693 --- /dev/null +++ b/branch/enrico-dependencies/organizing-projects/index.html @@ -0,0 +1,300 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Organizing your projects

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Objectives

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  • Get an overview on how to organize research projects

    • +
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+

Instructor note

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    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

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    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

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  • Use consistent and informative directory structure

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      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
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    • +

  • If you need to separate public/private, you can put them in public and private Git repos

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    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
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  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
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+

Tracking source code, data, and results

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  • All code is version controlled and goes in the src/ or source/ directory

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  • Include appropriate LICENSE file and information on software requirements

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  • You can also version control data files or input files under data/

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  • If data files are too large (or sensitive) to track, untrack them using .gitignore

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  • Intermediate files from the analysis are kept in processed_data/

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  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

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    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
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+ +
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+

Discussion on reproducibility

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+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

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+ +
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+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

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Reproducible publications

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  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

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      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

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    • HackMD or HedgeDoc: online collaborative Markdown editors

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    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

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    • +

  • Many tools exist to assist in making scholarly output reproducible:

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    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

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    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

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    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

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See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

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  • An organized project directory structure helps with reproducibility.

    • +
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+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/search/index.html b/branch/enrico-dependencies/search/index.html new file mode 100644 index 0000000..1b42337 --- /dev/null +++ b/branch/enrico-dependencies/search/index.html @@ -0,0 +1,157 @@ + + + + + + Search — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
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+ + + + + + + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/searchindex.js b/branch/enrico-dependencies/searchindex.js new file mode 100644 index 0000000..307cde7 --- /dev/null +++ b/branch/enrico-dependencies/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["dependencies", "environments", "exercises", "guide", "index", "intro", "motivation", "organizing-projects", "where-to-go", "workflow-management"], "filenames": ["dependencies.md", "environments.md", "exercises.md", "guide.md", "index.rst", "intro.md", "motivation.md", "organizing-projects.md", "where-to-go.md", "workflow-management.md"], "titles": ["Recording dependencies", "Recording environments", "List of exercises", "Instructor guide", "Reproducible research - Preparing code to be usable by you and others in the future", "Introduction - How it all connects", "Motivation", "Organizing your projects", "Where to go from here", "Recording computational steps"], "terms": {"how": [0, 1, 2, 4, 7, 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https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/enrico-dependencies/singlehtml/_static/basic.css b/branch/enrico-dependencies/singlehtml/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-dependencies/singlehtml/_static/check-solid.svg b/branch/enrico-dependencies/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/enrico-dependencies/singlehtml/_static/clipboard.min.js b/branch/enrico-dependencies/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/enrico-dependencies/singlehtml/_static/copybutton.css b/branch/enrico-dependencies/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/enrico-dependencies/singlehtml/_static/copybutton.js b/branch/enrico-dependencies/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/enrico-dependencies/singlehtml/_static/copybutton_funcs.js b/branch/enrico-dependencies/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/enrico-dependencies/singlehtml/_static/css/badge_only.css b/branch/enrico-dependencies/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- 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// [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/branch/enrico-dependencies/singlehtml/_static/minipres.js b/branch/enrico-dependencies/singlehtml/_static/minipres.js new file mode 100644 index 0000000..ad11c87 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/minipres.js @@ -0,0 +1,223 @@ +// Add goTo method to elements +// http://stackoverflow.com/questions/4801655/how-to-go-to-a-specific-element-on-page +(function($) { + $.fn.goTo = function() { + $('html, body').animate({ + scrollTop: $(this).offset().top //+ 'px' + }, 'fast'); + return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); // readthedocs version selector + + // Add other formats here. +} + + +var slideshow = minipres; + +if (window.location.search.match(/[?&](minipres|slideshow|pres)([=&]|$)/) ) { + //minipres() + window.addEventListener("load", minipres); +} else if (window.location.search.match(/[?&](plain)([=&]|$)/) ) { + window.addEventListener("load", hide); +} diff --git a/branch/enrico-dependencies/singlehtml/_static/minus.png b/branch/enrico-dependencies/singlehtml/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/branch/enrico-dependencies/singlehtml/_static/minus.png differ diff --git a/branch/enrico-dependencies/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css b/branch/enrico-dependencies/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css new file mode 100644 index 0000000..3356631 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css @@ -0,0 +1,2342 @@ +/* Variables */ +:root { + --mystnb-source-bg-color: #f7f7f7; + --mystnb-stdout-bg-color: #fcfcfc; + --mystnb-stderr-bg-color: #fdd; + --mystnb-traceback-bg-color: #fcfcfc; + --mystnb-source-border-color: #ccc; + --mystnb-source-margin-color: green; + --mystnb-stdout-border-color: #f7f7f7; + --mystnb-stderr-border-color: #f7f7f7; + --mystnb-traceback-border-color: #ffd6d6; + --mystnb-hide-prompt-opacity: 70%; + --mystnb-source-border-radius: .4em; + --mystnb-source-border-width: 1px; +} + +/* Whole cell */ +div.container.cell { + padding-left: 0; + margin-bottom: 1em; +} + +/* Removing all background formatting so we can control at the div level */ +.cell_input div.highlight, +.cell_output pre, +.cell_input pre, +.cell_output .output { + border: none; + box-shadow: none; +} + +.cell_output .output pre, +.cell_input pre { + margin: 0px; +} + +/* Input cells */ +div.cell div.cell_input, +div.cell details.above-input>summary { + padding-left: 0em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + background-color: var(--mystnb-source-bg-color); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; + border-radius: var(--mystnb-source-border-radius); +} + +div.cell_input>div, +div.cell_output div.output>div.highlight { + margin: 0em !important; + border: none !important; +} + +/* All cell outputs */ +.cell_output { + padding-left: 1em; + padding-right: 0em; + margin-top: 1em; +} + +/* Text outputs from cells */ +.cell_output .output.text_plain, +.cell_output .output.traceback, +.cell_output .output.stream, +.cell_output .output.stderr { + margin-top: 1em; + margin-bottom: 0em; + box-shadow: none; +} + +.cell_output .output.text_plain, +.cell_output .output.stream { + background: var(--mystnb-stdout-bg-color); + border: 1px solid var(--mystnb-stdout-border-color); +} + +.cell_output .output.stderr { + background: var(--mystnb-stderr-bg-color); + border: 1px solid var(--mystnb-stderr-border-color); +} + +.cell_output .output.traceback { + background: var(--mystnb-traceback-bg-color); + border: 1px solid var(--mystnb-traceback-border-color); +} + +/* Collapsible cell content */ +div.cell details.above-input div.cell_input { + border-top-left-radius: 0; + border-top-right-radius: 0; + border-top: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; +} + +div.cell div.cell_input.above-output-prompt { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; +} + +div.cell details.above-input>summary { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; + border-bottom: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; + padding-left: 1em; + margin-bottom: 0; +} + +div.cell details.above-output>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; +} + +div.cell details.below-input>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-top: none; + border-bottom-left-radius: var(--mystnb-source-border-radius); + border-bottom-right-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; +} + +div.cell details.hide>summary>span { + opacity: var(--mystnb-hide-prompt-opacity); +} + +div.cell details.hide[open]>summary>span.collapsed { + display: none; +} + +div.cell details.hide:not([open])>summary>span.expanded { + display: none; +} + +@keyframes collapsed-fade-in { + 0% { + opacity: 0; + } + + 100% { + opacity: 1; + } +} +div.cell details.hide[open]>summary~* { + -moz-animation: collapsed-fade-in 0.3s ease-in-out; + -webkit-animation: collapsed-fade-in 0.3s ease-in-out; + animation: collapsed-fade-in 0.3s ease-in-out; +} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/enrico-dependencies/singlehtml/_static/plus.png b/branch/enrico-dependencies/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/enrico-dependencies/singlehtml/_static/plus.png differ diff --git a/branch/enrico-dependencies/singlehtml/_static/pygments.css b/branch/enrico-dependencies/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ 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~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/enrico-dependencies/singlehtml/_static/sphinx_highlight.js b/branch/enrico-dependencies/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/enrico-dependencies/singlehtml/_static/sphinx_lesson.css b/branch/enrico-dependencies/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/enrico-dependencies/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/enrico-dependencies/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/enrico-dependencies/singlehtml/_static/tabs.css b/branch/enrico-dependencies/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/enrico-dependencies/singlehtml/_static/tabs.js b/branch/enrico-dependencies/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/enrico-dependencies/singlehtml/_static/term_role_formatting.css b/branch/enrico-dependencies/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/enrico-dependencies/singlehtml/_static/togglebutton.css b/branch/enrico-dependencies/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-dependencies/singlehtml/_static/togglebutton.js b/branch/enrico-dependencies/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/enrico-dependencies/singlehtml/index.html b/branch/enrico-dependencies/singlehtml/index.html new file mode 100644 index 0000000..d763cf3 --- /dev/null +++ b/branch/enrico-dependencies/singlehtml/index.html @@ -0,0 +1,1488 @@ + + + + + + + Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

We start from an existing conda environment. Try this either with your own project or inside the “coderefinery” conda +environment. For demonstration puprposes, you can also create an environment with:

+
$ conda env create -f myenv.yml
+
+
+

Where the file myenv.yml could have some python libraries with unspecified versions:

+
name: myenv
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - numpy
+  - pandas
+  - seaborn
+
+
+

After creating the environment we can activate it with

+
conda activate myenv
+
+
+

Now we can freeze the environment into a new YAML file with:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In the future — or on a different computer — we can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

What happens instead when you run the following command?

+
$ conda env export --from-history > environment_fromhistory.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+
+
+
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+
+
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/singlehtml/objects.inv b/branch/enrico-dependencies/singlehtml/objects.inv new file mode 100644 index 0000000..e7c16bd Binary files /dev/null and b/branch/enrico-dependencies/singlehtml/objects.inv differ diff --git a/branch/enrico-dependencies/where-to-go/index.html b/branch/enrico-dependencies/where-to-go/index.html new file mode 100644 index 0000000..8bb489f --- /dev/null +++ b/branch/enrico-dependencies/where-to-go/index.html @@ -0,0 +1,227 @@ + + + + + + + Where to go from here — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-dependencies/workflow-management/index.html b/branch/enrico-dependencies/workflow-management/index.html new file mode 100644 index 0000000..7c12ee4 --- /dev/null +++ b/branch/enrico-dependencies/workflow-management/index.html @@ -0,0 +1,393 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/.buildinfo b/branch/enrico-environments/.buildinfo new file mode 100644 index 0000000..94714cf --- /dev/null +++ b/branch/enrico-environments/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 639eb01f9a14f2c0189bf299fb057e86 +tags: d77d1c0d9ca2f4c8421862c7c5a0d620 diff --git a/branch/enrico-environments/.nojekyll b/branch/enrico-environments/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/branch/enrico-environments/_images/arrows.png b/branch/enrico-environments/_images/arrows.png new file mode 100644 index 0000000..2aa4a80 Binary files /dev/null and b/branch/enrico-environments/_images/arrows.png differ diff --git a/branch/enrico-environments/_images/dependency.png b/branch/enrico-environments/_images/dependency.png new file mode 100644 index 0000000..e07722d Binary files /dev/null and b/branch/enrico-environments/_images/dependency.png differ diff --git a/branch/enrico-environments/_images/docker_meme.jpg b/branch/enrico-environments/_images/docker_meme.jpg new file mode 100644 index 0000000..78d1b11 Binary files /dev/null and b/branch/enrico-environments/_images/docker_meme.jpg differ diff --git a/branch/enrico-environments/_images/libraries.png b/branch/enrico-environments/_images/libraries.png new file mode 100644 index 0000000..44202e3 Binary files /dev/null and b/branch/enrico-environments/_images/libraries.png differ diff --git a/branch/enrico-environments/_images/linux.png b/branch/enrico-environments/_images/linux.png new file mode 100644 index 0000000..1877b94 Binary files /dev/null and b/branch/enrico-environments/_images/linux.png differ diff --git a/branch/enrico-environments/_images/macos.png b/branch/enrico-environments/_images/macos.png new file mode 100644 index 0000000..3054c58 Binary files /dev/null and b/branch/enrico-environments/_images/macos.png differ diff --git a/branch/enrico-environments/_images/recipe.png b/branch/enrico-environments/_images/recipe.png new file mode 100644 index 0000000..1d6bd54 Binary files /dev/null and b/branch/enrico-environments/_images/recipe.png differ diff --git a/branch/enrico-environments/_images/repro-pyramid.png b/branch/enrico-environments/_images/repro-pyramid.png new file mode 100644 index 0000000..a8aec07 Binary files /dev/null and b/branch/enrico-environments/_images/repro-pyramid.png differ diff --git a/branch/enrico-environments/_images/reproducibility_nature.jpg b/branch/enrico-environments/_images/reproducibility_nature.jpg new file mode 100644 index 0000000..7967116 Binary files /dev/null and b/branch/enrico-environments/_images/reproducibility_nature.jpg differ diff --git a/branch/enrico-environments/_images/reproducible_research_plus_lessons.png b/branch/enrico-environments/_images/reproducible_research_plus_lessons.png new file mode 100644 index 0000000..fd092a6 Binary files /dev/null and b/branch/enrico-environments/_images/reproducible_research_plus_lessons.png differ diff --git a/branch/enrico-environments/_images/research_comic_phd.gif b/branch/enrico-environments/_images/research_comic_phd.gif new file mode 100644 index 0000000..f9be5a2 Binary files /dev/null and b/branch/enrico-environments/_images/research_comic_phd.gif differ diff --git a/branch/enrico-environments/_images/snakemake.png b/branch/enrico-environments/_images/snakemake.png new file mode 100644 index 0000000..ebe4f9e Binary files /dev/null and b/branch/enrico-environments/_images/snakemake.png differ diff --git a/branch/enrico-environments/_images/snakemake_dag.png b/branch/enrico-environments/_images/snakemake_dag.png new file mode 100644 index 0000000..eb4ae4e Binary files /dev/null and b/branch/enrico-environments/_images/snakemake_dag.png differ diff --git a/branch/enrico-environments/_images/windows.png b/branch/enrico-environments/_images/windows.png new file mode 100644 index 0000000..45d2668 Binary files /dev/null and b/branch/enrico-environments/_images/windows.png differ diff --git a/branch/enrico-environments/_sources/dependencies.md.txt b/branch/enrico-environments/_sources/dependencies.md.txt new file mode 100644 index 0000000..dba3a76 --- /dev/null +++ b/branch/enrico-environments/_sources/dependencies.md.txt @@ -0,0 +1,326 @@ +# Recording dependencies + +```{questions} +- How can we communicate different versions of software dependencies? +``` + +```{instructor-note} +- 10 min teaching +- 10 min demo +``` + +Our codes often depend on other codes that in turn depend on other codes ... + +- **Reproducibility**: We can version-control our code with Git but how should we version-control dependencies? + How can we capture and communicate dependencies? +- **Dependency hell**: Different codes on the same environment can have conflicting dependencies. + +```{figure} img/dependency.png +:alt: An image showing blocks (=codes) depending on each other for stability +:width: 60% + +From [xkcd - dependency](https://xkcd.com/2347/). Another image that might be familiar to some of you working with Python can be found on [xkcd - superfund](https://xkcd.com/1987/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Demo + +``````{challenge} Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +Answer in the collaborative document: + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} Dependencies-2: Create a time-capsule for the future +Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + Try this either with your own project or inside the "coderefinery" conda + environment: + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ conda env create -f environment.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` + + +```{keypoints} +- Recording dependencies with versions can make it easier for the next person to execute your code +- There are many tools to record dependencies +``` \ No newline at end of file diff --git a/branch/enrico-environments/_sources/environments.md.txt b/branch/enrico-environments/_sources/environments.md.txt new file mode 100644 index 0000000..b2d7424 --- /dev/null +++ b/branch/enrico-environments/_sources/environments.md.txt @@ -0,0 +1,324 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 10 min demo +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**. + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +## You may have use for containers in different ways + +- Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead! +- You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container! + - If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough. + +## The container recipe + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + + +````{exercise} (optional) Containers-2: Installing the impossible. + +When you are missing privileges for installing certain software tools, containers can come handy. +Here we build a Singularity/Apptainer container for installing `cowsay` and `lolcat` Linux programs. + +1. Make sure you have apptainer installed: + ```console + $ apptainer --version + ``` + +2. Make sure you set the apptainer cache and temporary folders. + ```console + $ mkdir ./cache/ + $ mkdir ./temp/ + $ export APPTAINER_CACHEDIR="./cache/" + $ export APPTAINER_TMPDIR="./temp/" + ``` + +3. Build the container from the following definition file above. + ```console + apptainer build cowsay.sif cowsay.def + ``` + +4. Let's test the container by entering into it with a shell terminal + ```console + $ apptainer shell cowsay.sif + ``` + +5. We can verify the installation. + ```console + $ cowsay "Hello world!"|lolcat + ``` + +```` + + + +````{exercise} (optional) Containers-3: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` + +## Resources for further learning + +- [Carpentries incubator lesson on Docker](https://carpentries-incubator.github.io/docker-introduction/) +- [Carpentries incubator lesson on Singularity/Apptainer](https://carpentries-incubator.github.io/singularity-introduction/) + + +```{keypoints} +- Containers can be helpful if complex setups are needed to running a specific software +- They can also be helpful for prototyping without "messing up" your own computing environment, or for running software that requires a different operating system than your own +``` diff --git a/branch/enrico-environments/_sources/exercises.md.txt b/branch/enrico-environments/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/branch/enrico-environments/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/branch/enrico-environments/_sources/guide.md.txt b/branch/enrico-environments/_sources/guide.md.txt new file mode 100644 index 0000000..97261f0 --- /dev/null +++ b/branch/enrico-environments/_sources/guide.md.txt @@ -0,0 +1,155 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +Two example schedules for this lesson: + +This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Overview of CR and how it all fits together +- 09:10 - 09:20 Reproducible research, [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:27 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:27 - 09:35 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) - discussion +- 09:35 - 10:00 Snakemake exercise (25 min) +- 10:00 - 10:10 Break +- 10:10 - 10:15 Summary of workflows and the exercise +- 10:15 - 10:30 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- 10:30 - 10:40 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) +- 10:40 - 11:00 Container-1 exercise (20 min) +- 11:00 - 11.05 Wrapup + +This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break): + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + diff --git a/branch/enrico-environments/_sources/index.rst.txt b/branch/enrico-environments/_sources/index.rst.txt new file mode 100644 index 0000000..05828e6 --- /dev/null +++ b/branch/enrico-environments/_sources/index.rst.txt @@ -0,0 +1,57 @@ +.. _index: + +Reproducible research - Preparing code to be usable by you and others in the future +=================================================================================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves and others. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - Be able to apply well organized directory structure for their project + - Understand that code can have dependencies, and know how to document them + - Be able to document computational steps, and have an idea when it can be useful + - Know about use cases for containers + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + intro.md + motivation.md + organizing-projects.md + workflow-management.md + dependencies.md + environments.md + where-to-go.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/branch/enrico-environments/_sources/intro.md.txt b/branch/enrico-environments/_sources/intro.md.txt new file mode 100644 index 0000000..6690f38 --- /dev/null +++ b/branch/enrico-environments/_sources/intro.md.txt @@ -0,0 +1,16 @@ +# Introduction - How it all connects + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +--- + +```{figure} img/reproducible_research_plus_lessons.png +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, ] + diff --git a/branch/enrico-environments/_sources/motivation.md.txt b/branch/enrico-environments/_sources/motivation.md.txt new file mode 100644 index 0000000..07d1f8e --- /dev/null +++ b/branch/enrico-environments/_sources/motivation.md.txt @@ -0,0 +1,74 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[Steeves, Vicky (2017) in "Reproducibility Librarianship," Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4] + +This also means that you can think about it from the beginning of your research life cycle! + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` + +```{keypoints} +- Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch +``` \ No newline at end of file diff --git a/branch/enrico-environments/_sources/organizing-projects.md.txt b/branch/enrico-environments/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..c46ad19 --- /dev/null +++ b/branch/enrico-environments/_sources/organizing-projects.md.txt @@ -0,0 +1,120 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the first steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* Check the [Git-intro lesson](https://coderefinery.github.io/git-intro/) for a reminder. + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in the collaborative document: + +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on the fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +## Some tools and templates + +- [R devtools](https://devtools.r-lib.org/) +- [Python cookiecutter template](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) +- [Reproducible research template](https://github.com/the-turing-way/reproducible-project-template) by the Turing Way + +More tools and templates in [Heidi Seibolds blog](https://heidiseibold.ck.page/posts/setting-up-a-fair-and-reproducible-project). + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration: + - [Overleaf](https://www.overleaf.com) or [Typst](https://typst.app/): online, collaborative LaTeX editor + - [Authorea](https://www.authorea.com): collaborative platform for preprints + - [HackMD](https://hackmd.io/) or [HedgeDoc](https://hedgedoc.org/): online collaborative Markdown editors + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as, see also our [Jupyter lesson](https://coderefinery.github.io/jupyter/) later in this workshop. + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + +```{keypoints} +- An organized project directory structure helps with reproducibility. +``` diff --git a/branch/enrico-environments/_sources/where-to-go.md.txt b/branch/enrico-environments/_sources/where-to-go.md.txt new file mode 100644 index 0000000..b524992 --- /dev/null +++ b/branch/enrico-environments/_sources/where-to-go.md.txt @@ -0,0 +1,53 @@ +# Where to go from here + +```{objectives} +- Understand when tools discussed in this episode can be useful +``` + +```{instructor-note} +- 10 min teaching/discussion +``` + +This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project. + +## Important for every project + +* Clear file structure for your project +* At least consider the possibility that someone, maybe you may want to reproduce your work + * Can you do something (small) to make it easier? + * If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help. + +## Workflow tools will maybe make sense in the future + +* In many cases, it is probably not needed +* You will want to consider workflow tools: + * When processing many files with many steps + * Steps or files may change + * Your main script, connecting your steps gets very long + * ... + +## When should I worry about dependencies? + +* Your code depends on multiple other packages +* You want to avoid questions like: "What do I need to install to run your code" +* You want help yourself running your code + * After a few years + * On a different computer + * ... + +## Containers seem amazing, but do I have use for them? + +* Maybe not yet, but knowing that you can ... + * Run Linux tools on your Windows computer + * Run different versions of same software on your computer + * Follow the "easy installation instructions" for an operating system that is not your own + * Get a fully configured environment instead of only installing a tool + * Share your setup and configurations with others +... can be very beneficial :) + + +```{keypoints} +- Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution. +- Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/branch/enrico-environments/_sources/workflow-management.md.txt b/branch/enrico-environments/_sources/workflow-management.md.txt new file mode 100644 index 0000000..83caaf6 --- /dev/null +++ b/branch/enrico-environments/_sources/workflow-management.md.txt @@ -0,0 +1,241 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 5 min teaching +- 15 min demo +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: + +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps. + +Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But **imagine having 4 steps and 500 books**. +How could we deal with this? + +As a first idea we could express the workflow with a script. The repository includes such script called `run_all.sh`. + +We can run it with: + +```console +$ bash run_all.sh +``` + +This is **imperative style**: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another. + +````{discussion} +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + + ```{solution} + The advantage of this solution compared to processing one by one is more automation: We can generate all. + This is not only easier, it is also less error-prone. + + Yes, the scripted solution can be reproducible. But could you easily run it e.g. on a Windows computer? + + If we had more steps and once steps start to be time-consuming, a limitation of + a scripted solution is that it tries to run all steps always. Rerunning only + part of the steps or only part of the input data requires us to outcomment or change lines in our script in between runs which can again become tedious and error-prone. + ``` +```` + +--- + +## Workflow tools + +Sometimes it may be helpful to go from imperative to declarative style. Rather than saying "do this and then that" we describe dependencies but we let the tool figure out the series of steps to produce results. + +### Example workflow tool: [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) + +Snakemake (inspired by [GNU Make](https://www.gnu.org/software/make/)) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition. + +--- + +## A demo + +````{prereq} Preparation +The exercise (below) and pre-exercise discussion uses the +word-count repository +() which we need to clone to work on it. + +If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the [CodeRefinery installation instruction page](https://coderefinery.github.io/installation/)), or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Install the necessary tools +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution in the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='code/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='code/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' + +``` + +We can see that Snakemake uses **declarative style**: +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Steps: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containing "shell". +``` +```` + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle **learning curve**. +- Free, open-source, and **installs easily** via conda or pip. +- **Cross-platform** (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them **in parallel**. +- Is is possible to define **isolated software environments** per rule, e.g. by adding `conda: 'environment.yml'` to a rule. +- Also possible to run workflows in Docker or Apptainer **containers** e.g. by adding `container: 'docker://some-org/some-tool#2.3.1'` to a rule. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is **completely general**. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + +Tools like Snakemake help us with **reproducibility** by supporting us with **automation**, **scalability** and **portability** of our workflows. + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. +- [Book on building reproducible analytical pipelines with R](https://raps-with-r.dev/) + +```{keypoints} +- Computational steps can be recorded in many ways +- Workflow tools can help, if there are many steps to be executed +``` diff --git a/branch/enrico-environments/_static/_sphinx_javascript_frameworks_compat.js b/branch/enrico-environments/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/enrico-environments/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; 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+} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-environments/_static/check-solid.svg b/branch/enrico-environments/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/enrico-environments/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/enrico-environments/_static/clipboard.min.js b/branch/enrico-environments/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/enrico-environments/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/enrico-environments/_static/copybutton.css b/branch/enrico-environments/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/enrico-environments/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/enrico-environments/_static/copybutton.js b/branch/enrico-environments/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/enrico-environments/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/enrico-environments/_static/copybutton_funcs.js b/branch/enrico-environments/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/enrico-environments/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/enrico-environments/_static/css/badge_only.css b/branch/enrico-environments/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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// [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/branch/enrico-environments/_static/minipres.js b/branch/enrico-environments/_static/minipres.js new file mode 100644 index 0000000..ad11c87 --- /dev/null +++ b/branch/enrico-environments/_static/minipres.js @@ -0,0 +1,223 @@ +// Add goTo method to elements +// http://stackoverflow.com/questions/4801655/how-to-go-to-a-specific-element-on-page +(function($) { + $.fn.goTo = function() { + $('html, body').animate({ + scrollTop: $(this).offset().top //+ 'px' + }, 'fast'); + return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); // readthedocs version selector + + // Add other formats here. +} + + +var slideshow = minipres; + +if (window.location.search.match(/[?&](minipres|slideshow|pres)([=&]|$)/) ) { + //minipres() + window.addEventListener("load", minipres); +} else if (window.location.search.match(/[?&](plain)([=&]|$)/) ) { + window.addEventListener("load", hide); +} diff --git a/branch/enrico-environments/_static/minus.png b/branch/enrico-environments/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/branch/enrico-environments/_static/minus.png differ diff --git a/branch/enrico-environments/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css b/branch/enrico-environments/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css new file mode 100644 index 0000000..3356631 --- /dev/null +++ b/branch/enrico-environments/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css @@ -0,0 +1,2342 @@ +/* Variables */ +:root { + --mystnb-source-bg-color: #f7f7f7; + --mystnb-stdout-bg-color: #fcfcfc; + --mystnb-stderr-bg-color: #fdd; + --mystnb-traceback-bg-color: #fcfcfc; + --mystnb-source-border-color: #ccc; + --mystnb-source-margin-color: green; + --mystnb-stdout-border-color: #f7f7f7; + --mystnb-stderr-border-color: #f7f7f7; + --mystnb-traceback-border-color: #ffd6d6; + --mystnb-hide-prompt-opacity: 70%; + --mystnb-source-border-radius: .4em; + --mystnb-source-border-width: 1px; +} + +/* Whole cell */ +div.container.cell { + padding-left: 0; + margin-bottom: 1em; +} + +/* Removing all background formatting so we can control at the div level */ +.cell_input div.highlight, +.cell_output pre, +.cell_input pre, +.cell_output .output { + border: none; + box-shadow: none; +} + +.cell_output .output pre, +.cell_input pre { + margin: 0px; +} + +/* Input cells */ +div.cell div.cell_input, +div.cell details.above-input>summary { + padding-left: 0em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + background-color: var(--mystnb-source-bg-color); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; + border-radius: var(--mystnb-source-border-radius); +} + +div.cell_input>div, +div.cell_output div.output>div.highlight { + margin: 0em !important; + border: none !important; +} + +/* All cell outputs */ +.cell_output { + padding-left: 1em; + padding-right: 0em; + margin-top: 1em; +} + +/* Text outputs from cells */ +.cell_output .output.text_plain, +.cell_output .output.traceback, +.cell_output .output.stream, +.cell_output .output.stderr { + margin-top: 1em; + margin-bottom: 0em; + box-shadow: none; +} + +.cell_output .output.text_plain, +.cell_output .output.stream { + background: var(--mystnb-stdout-bg-color); + border: 1px solid var(--mystnb-stdout-border-color); +} + +.cell_output .output.stderr { + background: var(--mystnb-stderr-bg-color); + border: 1px solid var(--mystnb-stderr-border-color); +} + +.cell_output .output.traceback { + background: var(--mystnb-traceback-bg-color); + border: 1px solid var(--mystnb-traceback-border-color); +} + +/* Collapsible cell content */ +div.cell details.above-input div.cell_input { + border-top-left-radius: 0; + border-top-right-radius: 0; + border-top: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; +} + +div.cell div.cell_input.above-output-prompt { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; +} + +div.cell details.above-input>summary { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; + border-bottom: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; + padding-left: 1em; + margin-bottom: 0; +} + +div.cell details.above-output>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; +} + +div.cell details.below-input>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-top: none; + border-bottom-left-radius: var(--mystnb-source-border-radius); + border-bottom-right-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; +} + +div.cell details.hide>summary>span { + opacity: var(--mystnb-hide-prompt-opacity); +} + +div.cell details.hide[open]>summary>span.collapsed { + display: none; +} + +div.cell details.hide:not([open])>summary>span.expanded { + display: none; +} + +@keyframes collapsed-fade-in { + 0% { + opacity: 0; + } + + 100% { + opacity: 1; + } +} +div.cell details.hide[open]>summary~* { + -moz-animation: collapsed-fade-in 0.3s ease-in-out; + -webkit-animation: collapsed-fade-in 0.3s ease-in-out; + animation: collapsed-fade-in 0.3s ease-in-out; +} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + 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.-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight 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+div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + 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background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/enrico-environments/_static/plus.png b/branch/enrico-environments/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/enrico-environments/_static/plus.png differ diff --git a/branch/enrico-environments/_static/pygments.css b/branch/enrico-environments/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/enrico-environments/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; font-style: italic } /* 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2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/enrico-environments/_static/sphinx_highlight.js b/branch/enrico-environments/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/enrico-environments/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/enrico-environments/_static/sphinx_lesson.css b/branch/enrico-environments/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/enrico-environments/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/enrico-environments/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/enrico-environments/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/enrico-environments/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/enrico-environments/_static/tabs.css b/branch/enrico-environments/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/enrico-environments/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/enrico-environments/_static/tabs.js b/branch/enrico-environments/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/enrico-environments/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/enrico-environments/_static/term_role_formatting.css b/branch/enrico-environments/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/enrico-environments/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/enrico-environments/_static/togglebutton.css b/branch/enrico-environments/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/enrico-environments/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-environments/_static/togglebutton.js b/branch/enrico-environments/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/enrico-environments/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/enrico-environments/dependencies/index.html b/branch/enrico-environments/dependencies/index.html new file mode 100644 index 0000000..f4c8dad --- /dev/null +++ b/branch/enrico-environments/dependencies/index.html @@ -0,0 +1,433 @@ + + + + + + + Recording dependencies — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/environments/index.html b/branch/enrico-environments/environments/index.html new file mode 100644 index 0000000..f6259af --- /dev/null +++ b/branch/enrico-environments/environments/index.html @@ -0,0 +1,480 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Installing the impossible.

+

When you are missing privileges for installing certain software tools, containers can come handy. +Here we build a Singularity/Apptainer container for installing cowsay and lolcat Linux programs.

+
    +

  1. Make sure you have apptainer installed:

    +
    $ apptainer --version
+
    +
    +
    2. +

  2. Make sure you set the apptainer cache and temporary folders.

    +
    $ mkdir ./cache/
+$ mkdir ./temp/
+$ export APPTAINER_CACHEDIR="./cache/"
+$ export APPTAINER_TMPDIR="./temp/"
+
    +
    +
    3. +

  3. Build the container from the following definition file above.

    +
    apptainer build cowsay.sif cowsay.def
+
    +
    +
    4. +

  4. Let’s test the container by entering into it with a shell terminal

    +
    $ apptainer shell cowsay.sif
+
    +
    +
    5. +

  5. We can verify the installation.

    +
    $ cowsay "Hello world!"|lolcat
+
    +
    +
    6. +
+
+
+

(optional) Containers-3: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/exercises/index.html b/branch/enrico-environments/exercises/index.html new file mode 100644 index 0000000..d3e3125 --- /dev/null +++ b/branch/enrico-environments/exercises/index.html @@ -0,0 +1,665 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording computational steps

+

In workflow-management.md:

+ +

In workflow-management.md:

+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording dependencies

+

In dependencies.md:

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

(optional) Containers-2: Installing the impossible.

+

When you are missing privileges for installing certain software tools, containers can come handy. +Here we build a Singularity/Apptainer container for installing cowsay and lolcat Linux programs.

+
    +

  1. Make sure you have apptainer installed:

    +
    $ apptainer --version
+
    +
    +
    2. +

  2. Make sure you set the apptainer cache and temporary folders.

    +
    $ mkdir ./cache/
+$ mkdir ./temp/
+$ export APPTAINER_CACHEDIR="./cache/"
+$ export APPTAINER_TMPDIR="./temp/"
+
    +
    +
    3. +

  3. Build the container from the following definition file above.

    +
    apptainer build cowsay.sif cowsay.def
+
    +
    +
    4. +

  4. Let’s test the container by entering into it with a shell terminal

    +
    $ apptainer shell cowsay.sif
+
    +
    +
    5. +

  5. We can verify the installation.

    +
    $ cowsay "Hello world!"|lolcat
+
    +
    +
    6. +
+
+

In environments.md:

+
+

(optional) Containers-3: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/genindex/index.html b/branch/enrico-environments/genindex/index.html new file mode 100644 index 0000000..040ed0f --- /dev/null +++ b/branch/enrico-environments/genindex/index.html @@ -0,0 +1,143 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/guide/index.html b/branch/enrico-environments/guide/index.html new file mode 100644 index 0000000..3ba180b --- /dev/null +++ b/branch/enrico-environments/guide/index.html @@ -0,0 +1,312 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/index.html b/branch/enrico-environments/index.html new file mode 100644 index 0000000..4273472 --- /dev/null +++ b/branch/enrico-environments/index.html @@ -0,0 +1,194 @@ + + + + + + + Reproducible research - Preparing code to be usable by you and others in the future — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research - Preparing code to be usable by you and others in the future
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/intro/index.html b/branch/enrico-environments/intro/index.html new file mode 100644 index 0000000..14bc998 --- /dev/null +++ b/branch/enrico-environments/intro/index.html @@ -0,0 +1,157 @@ + + + + + + + Introduction - How it all connects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/lesson.pdf b/branch/enrico-environments/lesson.pdf new file mode 100644 index 0000000..3d0b176 Binary files /dev/null and b/branch/enrico-environments/lesson.pdf differ diff --git a/branch/enrico-environments/motivation/index.html b/branch/enrico-environments/motivation/index.html new file mode 100644 index 0000000..a1fee3f --- /dev/null +++ b/branch/enrico-environments/motivation/index.html @@ -0,0 +1,217 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/objects.inv b/branch/enrico-environments/objects.inv new file mode 100644 index 0000000..e482281 Binary files /dev/null and b/branch/enrico-environments/objects.inv differ diff --git a/branch/enrico-environments/organizing-projects/index.html b/branch/enrico-environments/organizing-projects/index.html new file mode 100644 index 0000000..3ba7693 --- /dev/null +++ b/branch/enrico-environments/organizing-projects/index.html @@ -0,0 +1,300 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/search/index.html b/branch/enrico-environments/search/index.html new file mode 100644 index 0000000..1b42337 --- /dev/null +++ b/branch/enrico-environments/search/index.html @@ -0,0 +1,157 @@ + + + + + + Search — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/branch/enrico-environments/searchindex.js b/branch/enrico-environments/searchindex.js new file mode 100644 index 0000000..a423c87 --- /dev/null +++ b/branch/enrico-environments/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["dependencies", "environments", "exercises", "guide", "index", "intro", "motivation", "organizing-projects", "where-to-go", "workflow-management"], "filenames": ["dependencies.md", "environments.md", "exercises.md", "guide.md", "index.rst", "intro.md", "motivation.md", "organizing-projects.md", "where-to-go.md", "workflow-management.md"], "titles": ["Recording dependencies", "Recording environments", "List of exercises", "Instructor guide", "Reproducible research - Preparing code to be usable by you and others in the future", "Introduction - How it all connects", "Motivation", "Organizing your projects", "Where to go from here", "Recording computational steps"], "terms": {"how": [0, 1, 2, 4, 7, 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Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; 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+ margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; 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+ float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-environments/singlehtml/_static/check-solid.svg b/branch/enrico-environments/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/enrico-environments/singlehtml/_static/clipboard.min.js b/branch/enrico-environments/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/enrico-environments/singlehtml/_static/copybutton.css b/branch/enrico-environments/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/enrico-environments/singlehtml/_static/copybutton.js b/branch/enrico-environments/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/enrico-environments/singlehtml/_static/copybutton_funcs.js b/branch/enrico-environments/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/enrico-environments/singlehtml/_static/css/badge_only.css b/branch/enrico-environments/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- 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// [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/branch/enrico-environments/singlehtml/_static/minipres.js b/branch/enrico-environments/singlehtml/_static/minipres.js new file mode 100644 index 0000000..ad11c87 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/minipres.js @@ -0,0 +1,223 @@ +// Add goTo method to elements +// http://stackoverflow.com/questions/4801655/how-to-go-to-a-specific-element-on-page +(function($) { + $.fn.goTo = function() { + $('html, body').animate({ + scrollTop: $(this).offset().top //+ 'px' + }, 'fast'); + return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); // readthedocs version selector + + // Add other formats here. +} + + +var slideshow = minipres; + +if (window.location.search.match(/[?&](minipres|slideshow|pres)([=&]|$)/) ) { + //minipres() + window.addEventListener("load", minipres); +} else if (window.location.search.match(/[?&](plain)([=&]|$)/) ) { + window.addEventListener("load", hide); +} diff --git a/branch/enrico-environments/singlehtml/_static/minus.png b/branch/enrico-environments/singlehtml/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/branch/enrico-environments/singlehtml/_static/minus.png differ diff --git a/branch/enrico-environments/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css b/branch/enrico-environments/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css new file mode 100644 index 0000000..3356631 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css @@ -0,0 +1,2342 @@ +/* Variables */ +:root { + --mystnb-source-bg-color: #f7f7f7; + --mystnb-stdout-bg-color: #fcfcfc; + --mystnb-stderr-bg-color: #fdd; + --mystnb-traceback-bg-color: #fcfcfc; + --mystnb-source-border-color: #ccc; + --mystnb-source-margin-color: green; + --mystnb-stdout-border-color: #f7f7f7; + --mystnb-stderr-border-color: #f7f7f7; + --mystnb-traceback-border-color: #ffd6d6; + --mystnb-hide-prompt-opacity: 70%; + --mystnb-source-border-radius: .4em; + --mystnb-source-border-width: 1px; +} + +/* Whole cell */ +div.container.cell { + padding-left: 0; + margin-bottom: 1em; +} + +/* Removing all background formatting so we can control at the div level */ +.cell_input div.highlight, +.cell_output pre, +.cell_input pre, +.cell_output .output { + border: none; + box-shadow: none; +} + +.cell_output .output pre, +.cell_input pre { + margin: 0px; +} + +/* Input cells */ +div.cell div.cell_input, +div.cell details.above-input>summary { + padding-left: 0em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + background-color: var(--mystnb-source-bg-color); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; + border-radius: var(--mystnb-source-border-radius); +} + +div.cell_input>div, +div.cell_output div.output>div.highlight { + margin: 0em !important; + border: none !important; +} + +/* All cell outputs */ +.cell_output { + padding-left: 1em; + padding-right: 0em; + margin-top: 1em; +} + +/* Text outputs from cells */ +.cell_output .output.text_plain, +.cell_output .output.traceback, +.cell_output .output.stream, +.cell_output .output.stderr { + margin-top: 1em; + margin-bottom: 0em; + box-shadow: none; +} + +.cell_output .output.text_plain, +.cell_output .output.stream { + background: var(--mystnb-stdout-bg-color); + border: 1px solid var(--mystnb-stdout-border-color); +} + +.cell_output .output.stderr { + background: var(--mystnb-stderr-bg-color); + border: 1px solid var(--mystnb-stderr-border-color); +} + +.cell_output .output.traceback { + background: var(--mystnb-traceback-bg-color); + border: 1px solid var(--mystnb-traceback-border-color); +} + +/* Collapsible cell content */ +div.cell details.above-input div.cell_input { + border-top-left-radius: 0; + border-top-right-radius: 0; + border-top: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; +} + +div.cell div.cell_input.above-output-prompt { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; +} + +div.cell details.above-input>summary { + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; + border-bottom: var(--mystnb-source-border-width) var(--mystnb-source-border-color) dashed; + padding-left: 1em; + margin-bottom: 0; +} + +div.cell details.above-output>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; +} + +div.cell details.below-input>summary { + background-color: var(--mystnb-source-bg-color); + padding-left: 1em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; + border-top: none; + border-bottom-left-radius: var(--mystnb-source-border-radius); + border-bottom-right-radius: var(--mystnb-source-border-radius); + border-left-color: var(--mystnb-source-margin-color); + border-left-width: medium; +} + +div.cell details.hide>summary>span { + opacity: var(--mystnb-hide-prompt-opacity); +} + +div.cell details.hide[open]>summary>span.collapsed { + display: none; +} + +div.cell details.hide:not([open])>summary>span.expanded { + display: none; +} + +@keyframes collapsed-fade-in { + 0% { + opacity: 0; + } + + 100% { + opacity: 1; + } +} +div.cell details.hide[open]>summary~* { + -moz-animation: collapsed-fade-in 0.3s ease-in-out; + -webkit-animation: collapsed-fade-in 0.3s ease-in-out; + animation: collapsed-fade-in 0.3s ease-in-out; +} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/enrico-environments/singlehtml/_static/plus.png b/branch/enrico-environments/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/enrico-environments/singlehtml/_static/plus.png differ diff --git a/branch/enrico-environments/singlehtml/_static/pygments.css b/branch/enrico-environments/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ 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~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/enrico-environments/singlehtml/_static/sphinx_highlight.js b/branch/enrico-environments/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/enrico-environments/singlehtml/_static/sphinx_lesson.css b/branch/enrico-environments/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/enrico-environments/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/enrico-environments/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/enrico-environments/singlehtml/_static/tabs.css b/branch/enrico-environments/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/enrico-environments/singlehtml/_static/tabs.js b/branch/enrico-environments/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/enrico-environments/singlehtml/_static/term_role_formatting.css b/branch/enrico-environments/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/enrico-environments/singlehtml/_static/togglebutton.css b/branch/enrico-environments/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/enrico-environments/singlehtml/_static/togglebutton.js b/branch/enrico-environments/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/enrico-environments/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/enrico-environments/singlehtml/index.html b/branch/enrico-environments/singlehtml/index.html new file mode 100644 index 0000000..7ae5fe7 --- /dev/null +++ b/branch/enrico-environments/singlehtml/index.html @@ -0,0 +1,1499 @@ + + + + + + + Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Installing the impossible.

+

When you are missing privileges for installing certain software tools, containers can come handy. +Here we build a Singularity/Apptainer container for installing cowsay and lolcat Linux programs.

+
    +

  1. Make sure you have apptainer installed:

    +
    $ apptainer --version
+
    +
    +
    2. +

  2. Make sure you set the apptainer cache and temporary folders.

    +
    $ mkdir ./cache/
+$ mkdir ./temp/
+$ export APPTAINER_CACHEDIR="./cache/"
+$ export APPTAINER_TMPDIR="./temp/"
+
    +
    +
    3. +

  3. Build the container from the following definition file above.

    +
    apptainer build cowsay.sif cowsay.def
+
    +
    +
    4. +

  4. Let’s test the container by entering into it with a shell terminal

    +
    $ apptainer shell cowsay.sif
+
    +
    +
    5. +

  5. We can verify the installation.

    +
    $ cowsay "Hello world!"|lolcat
+
    +
    +
    6. +
+
+
+

(optional) Containers-3: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+
+
+
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+
+
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/singlehtml/objects.inv b/branch/enrico-environments/singlehtml/objects.inv new file mode 100644 index 0000000..e7c16bd Binary files /dev/null and b/branch/enrico-environments/singlehtml/objects.inv differ diff --git a/branch/enrico-environments/where-to-go/index.html b/branch/enrico-environments/where-to-go/index.html new file mode 100644 index 0000000..8bb489f --- /dev/null +++ b/branch/enrico-environments/where-to-go/index.html @@ -0,0 +1,227 @@ + + + + + + + Where to go from here — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/enrico-environments/workflow-management/index.html b/branch/enrico-environments/workflow-management/index.html new file mode 100644 index 0000000..7c12ee4 --- /dev/null +++ b/branch/enrico-environments/workflow-management/index.html @@ -0,0 +1,393 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/.buildinfo b/branch/main/.buildinfo new file mode 100644 index 0000000..7376126 --- /dev/null +++ b/branch/main/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. 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Another image that might be familiar to some of you working with Python can be found on [xkcd - superfund](https://xkcd.com/1987/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Demo + +``````{challenge} Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +Answer in the collaborative document: + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} Dependencies-2: Create a time-capsule for the future +Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + Try this either with your own project or inside the "coderefinery" conda + environment: + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ conda env create -f environment.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` + + +```{keypoints} +- Recording dependencies with versions can make it easier for the next person to execute your code +- There are many tools to record dependencies +``` \ No newline at end of file diff --git a/branch/main/_sources/environments.md.txt b/branch/main/_sources/environments.md.txt new file mode 100644 index 0000000..e36045f --- /dev/null +++ b/branch/main/_sources/environments.md.txt @@ -0,0 +1,286 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 10 min demo +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**. + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +## You may have use for containers in different ways + +- Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead! +- You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container! + - If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough. + +## The container recipe + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + +````{exercise} (optional) Containers-2: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` + +## Resources for further learning + +- [Carpentries incubator lesson on Docker](https://carpentries-incubator.github.io/docker-introduction/) +- [Carpentries incubator lesson on Singularity/Apptainer](https://carpentries-incubator.github.io/singularity-introduction/) + + +```{keypoints} +- Containers can be helpful if complex setups are needed to running a specific software +- They can also be helpful for prototyping without "messing up" your own computing environment, or for running software that requires a different operating system than your own +``` diff --git a/branch/main/_sources/exercises.md.txt b/branch/main/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/branch/main/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/branch/main/_sources/guide.md.txt b/branch/main/_sources/guide.md.txt new file mode 100644 index 0000000..97261f0 --- /dev/null +++ b/branch/main/_sources/guide.md.txt @@ -0,0 +1,155 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +Two example schedules for this lesson: + +This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Overview of CR and how it all fits together +- 09:10 - 09:20 Reproducible research, [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:27 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:27 - 09:35 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) - discussion +- 09:35 - 10:00 Snakemake exercise (25 min) +- 10:00 - 10:10 Break +- 10:10 - 10:15 Summary of workflows and the exercise +- 10:15 - 10:30 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- 10:30 - 10:40 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) +- 10:40 - 11:00 Container-1 exercise (20 min) +- 11:00 - 11.05 Wrapup + +This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break): + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + diff --git a/branch/main/_sources/index.rst.txt b/branch/main/_sources/index.rst.txt new file mode 100644 index 0000000..05828e6 --- /dev/null +++ b/branch/main/_sources/index.rst.txt @@ -0,0 +1,57 @@ +.. _index: + +Reproducible research - Preparing code to be usable by you and others in the future +=================================================================================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves and others. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - Be able to apply well organized directory structure for their project + - Understand that code can have dependencies, and know how to document them + - Be able to document computational steps, and have an idea when it can be useful + - Know about use cases for containers + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + intro.md + motivation.md + organizing-projects.md + workflow-management.md + dependencies.md + environments.md + where-to-go.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/branch/main/_sources/intro.md.txt b/branch/main/_sources/intro.md.txt new file mode 100644 index 0000000..6690f38 --- /dev/null +++ b/branch/main/_sources/intro.md.txt @@ -0,0 +1,16 @@ +# Introduction - How it all connects + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +--- + +```{figure} img/reproducible_research_plus_lessons.png +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, ] + diff --git a/branch/main/_sources/motivation.md.txt b/branch/main/_sources/motivation.md.txt new file mode 100644 index 0000000..07d1f8e --- /dev/null +++ b/branch/main/_sources/motivation.md.txt @@ -0,0 +1,74 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[Steeves, Vicky (2017) in "Reproducibility Librarianship," Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4] + +This also means that you can think about it from the beginning of your research life cycle! + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` + +```{keypoints} +- Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch +``` \ No newline at end of file diff --git a/branch/main/_sources/organizing-projects.md.txt b/branch/main/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..c46ad19 --- /dev/null +++ b/branch/main/_sources/organizing-projects.md.txt @@ -0,0 +1,120 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the first steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* Check the [Git-intro lesson](https://coderefinery.github.io/git-intro/) for a reminder. + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in the collaborative document: + +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on the fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +## Some tools and templates + +- [R devtools](https://devtools.r-lib.org/) +- [Python cookiecutter template](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) +- [Reproducible research template](https://github.com/the-turing-way/reproducible-project-template) by the Turing Way + +More tools and templates in [Heidi Seibolds blog](https://heidiseibold.ck.page/posts/setting-up-a-fair-and-reproducible-project). + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration: + - [Overleaf](https://www.overleaf.com) or [Typst](https://typst.app/): online, collaborative LaTeX editor + - [Authorea](https://www.authorea.com): collaborative platform for preprints + - [HackMD](https://hackmd.io/) or [HedgeDoc](https://hedgedoc.org/): online collaborative Markdown editors + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as, see also our [Jupyter lesson](https://coderefinery.github.io/jupyter/) later in this workshop. + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + +```{keypoints} +- An organized project directory structure helps with reproducibility. +``` diff --git a/branch/main/_sources/where-to-go.md.txt b/branch/main/_sources/where-to-go.md.txt new file mode 100644 index 0000000..b524992 --- /dev/null +++ b/branch/main/_sources/where-to-go.md.txt @@ -0,0 +1,53 @@ +# Where to go from here + +```{objectives} +- Understand when tools discussed in this episode can be useful +``` + +```{instructor-note} +- 10 min teaching/discussion +``` + +This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project. + +## Important for every project + +* Clear file structure for your project +* At least consider the possibility that someone, maybe you may want to reproduce your work + * Can you do something (small) to make it easier? + * If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help. + +## Workflow tools will maybe make sense in the future + +* In many cases, it is probably not needed +* You will want to consider workflow tools: + * When processing many files with many steps + * Steps or files may change + * Your main script, connecting your steps gets very long + * ... + +## When should I worry about dependencies? + +* Your code depends on multiple other packages +* You want to avoid questions like: "What do I need to install to run your code" +* You want help yourself running your code + * After a few years + * On a different computer + * ... + +## Containers seem amazing, but do I have use for them? + +* Maybe not yet, but knowing that you can ... + * Run Linux tools on your Windows computer + * Run different versions of same software on your computer + * Follow the "easy installation instructions" for an operating system that is not your own + * Get a fully configured environment instead of only installing a tool + * Share your setup and configurations with others +... can be very beneficial :) + + +```{keypoints} +- Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution. +- Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/branch/main/_sources/workflow-management.md.txt b/branch/main/_sources/workflow-management.md.txt new file mode 100644 index 0000000..83caaf6 --- /dev/null +++ b/branch/main/_sources/workflow-management.md.txt @@ -0,0 +1,241 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 5 min teaching +- 15 min demo +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: + +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps. + +Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But **imagine having 4 steps and 500 books**. +How could we deal with this? + +As a first idea we could express the workflow with a script. The repository includes such script called `run_all.sh`. + +We can run it with: + +```console +$ bash run_all.sh +``` + +This is **imperative style**: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another. + +````{discussion} +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + + ```{solution} + The advantage of this solution compared to processing one by one is more automation: We can generate all. + This is not only easier, it is also less error-prone. + + Yes, the scripted solution can be reproducible. But could you easily run it e.g. on a Windows computer? + + If we had more steps and once steps start to be time-consuming, a limitation of + a scripted solution is that it tries to run all steps always. Rerunning only + part of the steps or only part of the input data requires us to outcomment or change lines in our script in between runs which can again become tedious and error-prone. + ``` +```` + +--- + +## Workflow tools + +Sometimes it may be helpful to go from imperative to declarative style. Rather than saying "do this and then that" we describe dependencies but we let the tool figure out the series of steps to produce results. + +### Example workflow tool: [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) + +Snakemake (inspired by [GNU Make](https://www.gnu.org/software/make/)) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition. + +--- + +## A demo + +````{prereq} Preparation +The exercise (below) and pre-exercise discussion uses the +word-count repository +() which we need to clone to work on it. + +If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the [CodeRefinery installation instruction page](https://coderefinery.github.io/installation/)), or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Install the necessary tools +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution in the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='code/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='code/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' + +``` + +We can see that Snakemake uses **declarative style**: +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Steps: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containing "shell". +``` +```` + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle **learning curve**. +- Free, open-source, and **installs easily** via conda or pip. +- **Cross-platform** (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them **in parallel**. +- Is is possible to define **isolated software environments** per rule, e.g. by adding `conda: 'environment.yml'` to a rule. +- Also possible to run workflows in Docker or Apptainer **containers** e.g. by adding `container: 'docker://some-org/some-tool#2.3.1'` to a rule. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is **completely general**. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + +Tools like Snakemake help us with **reproducibility** by supporting us with **automation**, **scalability** and **portability** of our workflows. + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. +- [Book on building reproducible analytical pipelines with R](https://raps-with-r.dev/) + +```{keypoints} +- Computational steps can be recorded in many ways +- Workflow tools can help, if there are many steps to be executed +``` diff --git a/branch/main/_static/_sphinx_javascript_frameworks_compat.js b/branch/main/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/main/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/main/_static/basic.css b/branch/main/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/branch/main/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; 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+ margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/check-solid.svg b/branch/main/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/_static/clipboard.min.js b/branch/main/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/_static/copybutton.css b/branch/main/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/main/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/_static/copybutton.js b/branch/main/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/main/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/_static/copybutton_funcs.js b/branch/main/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + 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background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + 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background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight 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+if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/_static/sphinx_highlight.js b/branch/main/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/_static/sphinx_lesson.css b/branch/main/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/_static/tabs.css b/branch/main/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/_static/tabs.js b/branch/main/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/_static/term_role_formatting.css b/branch/main/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/_static/togglebutton.css b/branch/main/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/togglebutton.js b/branch/main/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/dependencies/index.html b/branch/main/dependencies/index.html new file mode 100644 index 0000000..1965948 --- /dev/null +++ b/branch/main/dependencies/index.html @@ -0,0 +1,434 @@ + + + + + + + Recording dependencies — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/environments/index.html b/branch/main/environments/index.html new file mode 100644 index 0000000..c70062f --- /dev/null +++ b/branch/main/environments/index.html @@ -0,0 +1,446 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/exercises/index.html b/branch/main/exercises/index.html new file mode 100644 index 0000000..b0faf96 --- /dev/null +++ b/branch/main/exercises/index.html @@ -0,0 +1,630 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording computational steps

+

In workflow-management.md:

+ +

In workflow-management.md:

+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording dependencies

+

In dependencies.md:

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/genindex/index.html b/branch/main/genindex/index.html new file mode 100644 index 0000000..3bacb50 --- /dev/null +++ b/branch/main/genindex/index.html @@ -0,0 +1,144 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/guide/index.html b/branch/main/guide/index.html new file mode 100644 index 0000000..859e3fe --- /dev/null +++ b/branch/main/guide/index.html @@ -0,0 +1,313 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/index.html b/branch/main/index.html new file mode 100644 index 0000000..f49fd57 --- /dev/null +++ b/branch/main/index.html @@ -0,0 +1,195 @@ + + + + + + + Reproducible research - Preparing code to be usable by you and others in the future — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research - Preparing code to be usable by you and others in the future
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/intro/index.html b/branch/main/intro/index.html new file mode 100644 index 0000000..c019e21 --- /dev/null +++ b/branch/main/intro/index.html @@ -0,0 +1,158 @@ + + + + + + + Introduction - How it all connects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/lesson.pdf b/branch/main/lesson.pdf new file mode 100644 index 0000000..06413f9 Binary files /dev/null and b/branch/main/lesson.pdf differ diff --git a/branch/main/motivation/index.html b/branch/main/motivation/index.html new file mode 100644 index 0000000..a6a7cf9 --- /dev/null +++ b/branch/main/motivation/index.html @@ -0,0 +1,218 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/objects.inv b/branch/main/objects.inv new file mode 100644 index 0000000..e482281 Binary files /dev/null and b/branch/main/objects.inv differ diff --git a/branch/main/organizing-projects/index.html b/branch/main/organizing-projects/index.html new file mode 100644 index 0000000..c74ad78 --- /dev/null +++ b/branch/main/organizing-projects/index.html @@ -0,0 +1,301 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/search/index.html b/branch/main/search/index.html new file mode 100644 index 0000000..a7c0234 --- /dev/null +++ b/branch/main/search/index.html @@ -0,0 +1,158 @@ + + + + + + Search — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/branch/main/searchindex.js b/branch/main/searchindex.js new file mode 100644 index 0000000..e656bb8 --- /dev/null +++ b/branch/main/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["dependencies", "environments", "exercises", "guide", "index", "intro", "motivation", "organizing-projects", "where-to-go", "workflow-management"], "filenames": ["dependencies.md", "environments.md", "exercises.md", "guide.md", "index.rst", "intro.md", "motivation.md", "organizing-projects.md", "where-to-go.md", "workflow-management.md"], "titles": ["Recording dependencies", "Recording environments", "List of exercises", "Instructor guide", "Reproducible research - Preparing code to be usable by you and others in the future", "Introduction - How it all connects", "Motivation", "Organizing your projects", "Where to go from here", "Recording computational steps"], "terms": {"how": [0, 1, 2, 4, 7, 9], "can": [0, 2, 3, 4, 6, 7, 8, 9], "we": 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+} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/check-solid.svg b/branch/main/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/singlehtml/_static/clipboard.min.js b/branch/main/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/singlehtml/_static/copybutton.css b/branch/main/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/singlehtml/_static/copybutton.js b/branch/main/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/singlehtml/_static/copybutton_funcs.js b/branch/main/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/main/singlehtml/_static/plus.png b/branch/main/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/main/singlehtml/_static/plus.png differ diff --git a/branch/main/singlehtml/_static/pygments.css b/branch/main/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/main/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ 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+.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/main/singlehtml/_static/searchtools.js b/branch/main/singlehtml/_static/searchtools.js new file mode 100644 index 0000000..7918c3f --- /dev/null +++ b/branch/main/singlehtml/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/singlehtml/_static/sphinx_highlight.js b/branch/main/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/singlehtml/_static/sphinx_lesson.css b/branch/main/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/singlehtml/_static/tabs.css b/branch/main/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/singlehtml/_static/tabs.js b/branch/main/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/singlehtml/_static/term_role_formatting.css b/branch/main/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/singlehtml/_static/togglebutton.css b/branch/main/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/togglebutton.js b/branch/main/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/singlehtml/index.html b/branch/main/singlehtml/index.html new file mode 100644 index 0000000..4c9128f --- /dev/null +++ b/branch/main/singlehtml/index.html @@ -0,0 +1,1465 @@ + + + + + + + Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+
+
+
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+
+
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/singlehtml/objects.inv b/branch/main/singlehtml/objects.inv new file mode 100644 index 0000000..e7c16bd Binary files /dev/null and b/branch/main/singlehtml/objects.inv differ diff --git a/branch/main/where-to-go/index.html b/branch/main/where-to-go/index.html new file mode 100644 index 0000000..bdc8a2d --- /dev/null +++ b/branch/main/where-to-go/index.html @@ -0,0 +1,228 @@ + + + + + + + Where to go from here — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

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    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

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    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
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+
+ + +
+
+ +
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+
+ + + + \ No newline at end of file diff --git a/branch/main/workflow-management/index.html b/branch/main/workflow-management/index.html new file mode 100644 index 0000000..1c9f0d7 --- /dev/null +++ b/branch/main/workflow-management/index.html @@ -0,0 +1,394 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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+
+ +
+
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+
+ +
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
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+
+
+ + +
+
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Another image that might be familiar to some of you working with Python can be found on [xkcd - superfund](https://xkcd.com/1987/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Demo + +``````{challenge} Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +Answer in the collaborative document: + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} Dependencies-2: Create a time-capsule for the future +Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + Try this either with your own project or inside the "coderefinery" conda + environment: + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ conda env create -f environment.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` + + +```{keypoints} +- Recording dependencies with versions can make it easier for the next person to execute your code +- There are many tools to record dependencies +``` \ No newline at end of file diff --git a/branch/swi_march24/_sources/environments.md.txt b/branch/swi_march24/_sources/environments.md.txt new file mode 100644 index 0000000..e36045f --- /dev/null +++ b/branch/swi_march24/_sources/environments.md.txt @@ -0,0 +1,286 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 10 min demo +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**. + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +## You may have use for containers in different ways + +- Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead! +- You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container! + - If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough. + +## The container recipe + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + +````{exercise} (optional) Containers-2: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` + +## Resources for further learning + +- [Carpentries incubator lesson on Docker](https://carpentries-incubator.github.io/docker-introduction/) +- [Carpentries incubator lesson on Singularity/Apptainer](https://carpentries-incubator.github.io/singularity-introduction/) + + +```{keypoints} +- Containers can be helpful if complex setups are needed to running a specific software +- They can also be helpful for prototyping without "messing up" your own computing environment, or for running software that requires a different operating system than your own +``` diff --git a/branch/swi_march24/_sources/exercises.md.txt b/branch/swi_march24/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/branch/swi_march24/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/branch/swi_march24/_sources/guide.md.txt b/branch/swi_march24/_sources/guide.md.txt new file mode 100644 index 0000000..97261f0 --- /dev/null +++ b/branch/swi_march24/_sources/guide.md.txt @@ -0,0 +1,155 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +Two example schedules for this lesson: + +This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Overview of CR and how it all fits together +- 09:10 - 09:20 Reproducible research, [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:27 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:27 - 09:35 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) - discussion +- 09:35 - 10:00 Snakemake exercise (25 min) +- 10:00 - 10:10 Break +- 10:10 - 10:15 Summary of workflows and the exercise +- 10:15 - 10:30 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- 10:30 - 10:40 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) +- 10:40 - 11:00 Container-1 exercise (20 min) +- 11:00 - 11.05 Wrapup + +This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break): + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + diff --git a/branch/swi_march24/_sources/index.rst.txt b/branch/swi_march24/_sources/index.rst.txt new file mode 100644 index 0000000..05828e6 --- /dev/null +++ b/branch/swi_march24/_sources/index.rst.txt @@ -0,0 +1,57 @@ +.. _index: + +Reproducible research - Preparing code to be usable by you and others in the future +=================================================================================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves and others. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - Be able to apply well organized directory structure for their project + - Understand that code can have dependencies, and know how to document them + - Be able to document computational steps, and have an idea when it can be useful + - Know about use cases for containers + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + intro.md + motivation.md + organizing-projects.md + workflow-management.md + dependencies.md + environments.md + where-to-go.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/branch/swi_march24/_sources/intro.md.txt b/branch/swi_march24/_sources/intro.md.txt new file mode 100644 index 0000000..6690f38 --- /dev/null +++ b/branch/swi_march24/_sources/intro.md.txt @@ -0,0 +1,16 @@ +# Introduction - How it all connects + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +--- + +```{figure} img/reproducible_research_plus_lessons.png +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, ] + diff --git a/branch/swi_march24/_sources/motivation.md.txt b/branch/swi_march24/_sources/motivation.md.txt new file mode 100644 index 0000000..07d1f8e --- /dev/null +++ b/branch/swi_march24/_sources/motivation.md.txt @@ -0,0 +1,74 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[Steeves, Vicky (2017) in "Reproducibility Librarianship," Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4] + +This also means that you can think about it from the beginning of your research life cycle! + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` + +```{keypoints} +- Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch +``` \ No newline at end of file diff --git a/branch/swi_march24/_sources/organizing-projects.md.txt b/branch/swi_march24/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..c46ad19 --- /dev/null +++ b/branch/swi_march24/_sources/organizing-projects.md.txt @@ -0,0 +1,120 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the first steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* Check the [Git-intro lesson](https://coderefinery.github.io/git-intro/) for a reminder. + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in the collaborative document: + +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on the fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +## Some tools and templates + +- [R devtools](https://devtools.r-lib.org/) +- [Python cookiecutter template](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) +- [Reproducible research template](https://github.com/the-turing-way/reproducible-project-template) by the Turing Way + +More tools and templates in [Heidi Seibolds blog](https://heidiseibold.ck.page/posts/setting-up-a-fair-and-reproducible-project). + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration: + - [Overleaf](https://www.overleaf.com) or [Typst](https://typst.app/): online, collaborative LaTeX editor + - [Authorea](https://www.authorea.com): collaborative platform for preprints + - [HackMD](https://hackmd.io/) or [HedgeDoc](https://hedgedoc.org/): online collaborative Markdown editors + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as, see also our [Jupyter lesson](https://coderefinery.github.io/jupyter/) later in this workshop. + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + +```{keypoints} +- An organized project directory structure helps with reproducibility. +``` diff --git a/branch/swi_march24/_sources/where-to-go.md.txt b/branch/swi_march24/_sources/where-to-go.md.txt new file mode 100644 index 0000000..b524992 --- /dev/null +++ b/branch/swi_march24/_sources/where-to-go.md.txt @@ -0,0 +1,53 @@ +# Where to go from here + +```{objectives} +- Understand when tools discussed in this episode can be useful +``` + +```{instructor-note} +- 10 min teaching/discussion +``` + +This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project. + +## Important for every project + +* Clear file structure for your project +* At least consider the possibility that someone, maybe you may want to reproduce your work + * Can you do something (small) to make it easier? + * If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help. + +## Workflow tools will maybe make sense in the future + +* In many cases, it is probably not needed +* You will want to consider workflow tools: + * When processing many files with many steps + * Steps or files may change + * Your main script, connecting your steps gets very long + * ... + +## When should I worry about dependencies? + +* Your code depends on multiple other packages +* You want to avoid questions like: "What do I need to install to run your code" +* You want help yourself running your code + * After a few years + * On a different computer + * ... + +## Containers seem amazing, but do I have use for them? + +* Maybe not yet, but knowing that you can ... + * Run Linux tools on your Windows computer + * Run different versions of same software on your computer + * Follow the "easy installation instructions" for an operating system that is not your own + * Get a fully configured environment instead of only installing a tool + * Share your setup and configurations with others +... can be very beneficial :) + + +```{keypoints} +- Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution. +- Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/branch/swi_march24/_sources/workflow-management.md.txt b/branch/swi_march24/_sources/workflow-management.md.txt new file mode 100644 index 0000000..83caaf6 --- /dev/null +++ b/branch/swi_march24/_sources/workflow-management.md.txt @@ -0,0 +1,241 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 5 min teaching +- 15 min demo +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: + +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps. + +Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But **imagine having 4 steps and 500 books**. +How could we deal with this? + +As a first idea we could express the workflow with a script. The repository includes such script called `run_all.sh`. + +We can run it with: + +```console +$ bash run_all.sh +``` + +This is **imperative style**: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another. + +````{discussion} +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + + ```{solution} + The advantage of this solution compared to processing one by one is more automation: We can generate all. + This is not only easier, it is also less error-prone. + + Yes, the scripted solution can be reproducible. But could you easily run it e.g. on a Windows computer? + + If we had more steps and once steps start to be time-consuming, a limitation of + a scripted solution is that it tries to run all steps always. Rerunning only + part of the steps or only part of the input data requires us to outcomment or change lines in our script in between runs which can again become tedious and error-prone. + ``` +```` + +--- + +## Workflow tools + +Sometimes it may be helpful to go from imperative to declarative style. Rather than saying "do this and then that" we describe dependencies but we let the tool figure out the series of steps to produce results. + +### Example workflow tool: [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) + +Snakemake (inspired by [GNU Make](https://www.gnu.org/software/make/)) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition. + +--- + +## A demo + +````{prereq} Preparation +The exercise (below) and pre-exercise discussion uses the +word-count repository +() which we need to clone to work on it. + +If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the [CodeRefinery installation instruction page](https://coderefinery.github.io/installation/)), or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Install the necessary tools +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution in the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='code/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='code/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' + +``` + +We can see that Snakemake uses **declarative style**: +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Steps: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containing "shell". +``` +```` + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle **learning curve**. +- Free, open-source, and **installs easily** via conda or pip. +- **Cross-platform** (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them **in parallel**. +- Is is possible to define **isolated software environments** per rule, e.g. by adding `conda: 'environment.yml'` to a rule. +- Also possible to run workflows in Docker or Apptainer **containers** e.g. by adding `container: 'docker://some-org/some-tool#2.3.1'` to a rule. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is **completely general**. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + +Tools like Snakemake help us with **reproducibility** by supporting us with **automation**, **scalability** and **portability** of our workflows. + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. +- [Book on building reproducible analytical pipelines with R](https://raps-with-r.dev/) + +```{keypoints} +- Computational steps can be recorded in many ways +- Workflow tools can help, if there are many steps to be executed +``` diff --git a/branch/swi_march24/_static/_sphinx_javascript_frameworks_compat.js b/branch/swi_march24/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/swi_march24/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_march24/_static/check-solid.svg b/branch/swi_march24/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/swi_march24/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/swi_march24/_static/clipboard.min.js b/branch/swi_march24/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/swi_march24/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/swi_march24/_static/copybutton.css b/branch/swi_march24/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/swi_march24/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/swi_march24/_static/copybutton.js b/branch/swi_march24/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/swi_march24/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/swi_march24/_static/copybutton_funcs.js b/branch/swi_march24/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/swi_march24/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/swi_march24/_static/css/badge_only.css b/branch/swi_march24/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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+ stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/branch/swi_march24/_static/minipres.js b/branch/swi_march24/_static/minipres.js new file mode 100644 index 0000000..ad11c87 --- /dev/null +++ b/branch/swi_march24/_static/minipres.js @@ -0,0 +1,223 @@ +// Add goTo method to elements +// http://stackoverflow.com/questions/4801655/how-to-go-to-a-specific-element-on-page +(function($) { + $.fn.goTo = function() { + $('html, body').animate({ + scrollTop: $(this).offset().top //+ 'px' + }, 'fast'); + return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); // readthedocs version selector + + // Add other formats here. +} + + +var slideshow = minipres; + +if (window.location.search.match(/[?&](minipres|slideshow|pres)([=&]|$)/) ) { + //minipres() + window.addEventListener("load", minipres); +} else if (window.location.search.match(/[?&](plain)([=&]|$)/) ) { + window.addEventListener("load", hide); +} diff --git a/branch/swi_march24/_static/minus.png b/branch/swi_march24/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/branch/swi_march24/_static/minus.png differ diff --git a/branch/swi_march24/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css b/branch/swi_march24/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css new file mode 100644 index 0000000..3356631 --- /dev/null +++ b/branch/swi_march24/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css @@ -0,0 +1,2342 @@ +/* Variables */ +:root { + --mystnb-source-bg-color: #f7f7f7; 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/swi_march24/_static/plus.png b/branch/swi_march24/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/swi_march24/_static/plus.png differ diff --git a/branch/swi_march24/_static/pygments.css b/branch/swi_march24/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/swi_march24/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } 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+ * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/swi_march24/_static/sphinx_highlight.js b/branch/swi_march24/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/swi_march24/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/swi_march24/_static/sphinx_lesson.css b/branch/swi_march24/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/swi_march24/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/swi_march24/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/swi_march24/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/swi_march24/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/swi_march24/_static/tabs.css b/branch/swi_march24/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/swi_march24/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/swi_march24/_static/tabs.js b/branch/swi_march24/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/swi_march24/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/swi_march24/_static/term_role_formatting.css b/branch/swi_march24/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/swi_march24/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/swi_march24/_static/togglebutton.css b/branch/swi_march24/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/swi_march24/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_march24/_static/togglebutton.js b/branch/swi_march24/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/swi_march24/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/swi_march24/dependencies/index.html b/branch/swi_march24/dependencies/index.html new file mode 100644 index 0000000..f4c8dad --- /dev/null +++ b/branch/swi_march24/dependencies/index.html @@ -0,0 +1,433 @@ + + + + + + + Recording dependencies — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/environments/index.html b/branch/swi_march24/environments/index.html new file mode 100644 index 0000000..b52ec23 --- /dev/null +++ b/branch/swi_march24/environments/index.html @@ -0,0 +1,445 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/exercises/index.html b/branch/swi_march24/exercises/index.html new file mode 100644 index 0000000..8ee52d7 --- /dev/null +++ b/branch/swi_march24/exercises/index.html @@ -0,0 +1,629 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording computational steps

+

In workflow-management.md:

+ +

In workflow-management.md:

+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording dependencies

+

In dependencies.md:

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/genindex/index.html b/branch/swi_march24/genindex/index.html new file mode 100644 index 0000000..040ed0f --- /dev/null +++ b/branch/swi_march24/genindex/index.html @@ -0,0 +1,143 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/guide/index.html b/branch/swi_march24/guide/index.html new file mode 100644 index 0000000..3ba180b --- /dev/null +++ b/branch/swi_march24/guide/index.html @@ -0,0 +1,312 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/index.html b/branch/swi_march24/index.html new file mode 100644 index 0000000..4273472 --- /dev/null +++ b/branch/swi_march24/index.html @@ -0,0 +1,194 @@ + + + + + + + Reproducible research - Preparing code to be usable by you and others in the future — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research - Preparing code to be usable by you and others in the future
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/intro/index.html b/branch/swi_march24/intro/index.html new file mode 100644 index 0000000..14bc998 --- /dev/null +++ b/branch/swi_march24/intro/index.html @@ -0,0 +1,157 @@ + + + + + + + Introduction - How it all connects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/lesson.pdf b/branch/swi_march24/lesson.pdf new file mode 100644 index 0000000..fc225cc Binary files /dev/null and b/branch/swi_march24/lesson.pdf differ diff --git a/branch/swi_march24/motivation/index.html b/branch/swi_march24/motivation/index.html new file mode 100644 index 0000000..a1fee3f --- /dev/null +++ b/branch/swi_march24/motivation/index.html @@ -0,0 +1,217 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/objects.inv b/branch/swi_march24/objects.inv new file mode 100644 index 0000000..e482281 Binary files /dev/null and b/branch/swi_march24/objects.inv differ diff --git a/branch/swi_march24/organizing-projects/index.html b/branch/swi_march24/organizing-projects/index.html new file mode 100644 index 0000000..3ba7693 --- /dev/null +++ b/branch/swi_march24/organizing-projects/index.html @@ -0,0 +1,300 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/search/index.html b/branch/swi_march24/search/index.html new file mode 100644 index 0000000..1b42337 --- /dev/null +++ b/branch/swi_march24/search/index.html @@ -0,0 +1,157 @@ + + + + + + Search — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
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Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/swi_march24/singlehtml/_static/basic.css b/branch/swi_march24/singlehtml/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; 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+ margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_march24/singlehtml/_static/check-solid.svg b/branch/swi_march24/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/swi_march24/singlehtml/_static/clipboard.min.js b/branch/swi_march24/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/swi_march24/singlehtml/_static/copybutton.css b/branch/swi_march24/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/swi_march24/singlehtml/_static/copybutton.js b/branch/swi_march24/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/swi_march24/singlehtml/_static/copybutton_funcs.js b/branch/swi_march24/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/swi_march24/singlehtml/_static/css/badge_only.css b/branch/swi_march24/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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+ stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/branch/swi_march24/singlehtml/_static/minipres.js b/branch/swi_march24/singlehtml/_static/minipres.js new file mode 100644 index 0000000..ad11c87 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/minipres.js @@ -0,0 +1,223 @@ +// Add goTo method to elements +// http://stackoverflow.com/questions/4801655/how-to-go-to-a-specific-element-on-page +(function($) { + $.fn.goTo = function() { + $('html, body').animate({ + scrollTop: $(this).offset().top //+ 'px' + }, 'fast'); + return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/swi_march24/singlehtml/_static/plus.png b/branch/swi_march24/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/swi_march24/singlehtml/_static/plus.png differ diff --git a/branch/swi_march24/singlehtml/_static/pygments.css b/branch/swi_march24/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; 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#A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/swi_march24/singlehtml/_static/searchtools.js b/branch/swi_march24/singlehtml/_static/searchtools.js new file mode 100644 index 0000000..7918c3f --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/swi_march24/singlehtml/_static/sphinx_highlight.js b/branch/swi_march24/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/swi_march24/singlehtml/_static/sphinx_lesson.css b/branch/swi_march24/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/swi_march24/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/swi_march24/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/swi_march24/singlehtml/_static/tabs.css b/branch/swi_march24/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/swi_march24/singlehtml/_static/tabs.js b/branch/swi_march24/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/swi_march24/singlehtml/_static/term_role_formatting.css b/branch/swi_march24/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/swi_march24/singlehtml/_static/togglebutton.css b/branch/swi_march24/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_march24/singlehtml/_static/togglebutton.js b/branch/swi_march24/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/swi_march24/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/swi_march24/singlehtml/index.html b/branch/swi_march24/singlehtml/index.html new file mode 100644 index 0000000..68cfb25 --- /dev/null +++ b/branch/swi_march24/singlehtml/index.html @@ -0,0 +1,1464 @@ + + + + + + + Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+
+
+
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+
+
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/singlehtml/objects.inv b/branch/swi_march24/singlehtml/objects.inv new file mode 100644 index 0000000..e7c16bd Binary files /dev/null and b/branch/swi_march24/singlehtml/objects.inv differ diff --git a/branch/swi_march24/where-to-go/index.html b/branch/swi_march24/where-to-go/index.html new file mode 100644 index 0000000..8bb489f --- /dev/null +++ b/branch/swi_march24/where-to-go/index.html @@ -0,0 +1,227 @@ + + + + + + + Where to go from here — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_march24/workflow-management/index.html b/branch/swi_march24/workflow-management/index.html new file mode 100644 index 0000000..7c12ee4 --- /dev/null +++ b/branch/swi_march24/workflow-management/index.html @@ -0,0 +1,393 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/.buildinfo b/branch/swi_snakemake/.buildinfo new file mode 100644 index 0000000..94714cf --- /dev/null +++ b/branch/swi_snakemake/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. 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+``` + +```{instructor-note} +- 10 min teaching +- 20 min exercises +``` +Our codes often depend on other codes that in turn depend on other codes ... + +- **Reproducibility**: We can version-control our code with Git but how should we version-control dependencies? + How can we capture and communicate dependencies? +- **Dependency hell**: Different codes on the same environment can have conflicting dependencies. + +```{figure} img/python_environment.png +:alt: An image showing a mess of dependecies in a Python environment +:width: 60% + +From [xkcd](https://xkcd.com/). +``` + +````{discussion} Kitchen analogy +- Software <-> recipe +- Data <-> ingredients +- Libraries <-> cooking books/blogs + +```{figure} img/kitchen/recipe.png +:alt: Cooking recipe in an unfamiliar language +:width: 50% + +Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0] +``` + +```{figure} img/kitchen/libraries.png +:alt: Kitchen with few open cooking books +:width: 50% + +When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0] +``` +```` + +--- + +## Tools and what problems they try to solve + +**Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv**, ..., these tools try to solve the following problems: +- **Defining a specific set of dependencies**, possibly with well defined versions +- **Installing those dependencies** mostly automatically +- **Recording the versions** for all dependencies +- **Isolate environments** + - On your computer for projects so they can use different software + - Isolate environments on computers with many users (and allow self-installations) +- Using **different Python/R versions** per project +- Provide tools and services to **share packages** + +Isolated environments are also useful because they help you make sure +that you know your dependencies! + +**If things go wrong, you can delete and re-create** - much better +than debugging. The more often you re-create your environment, the +more reproducible it is. + +--- + +## Exercises + +``````{challenge} (optional) Dependencies-1: Time-capsule of dependencies +Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it. + +Answer in the collaborative document: + +- Which version do you expect to be easiest to re-run? Why? +- What problems do you anticipate in each solution? + + `````{tabs} + ````{group-tab} Conda + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy + - numpy + - sympy + - click + - python + - pip + - pip: + - git+https://github.com/someuser/someproject.git@master + - git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - pip + - pip: + - git+https://github.com/someuser/someproject.git@d7b2c7e + - git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `environment.yml` file with: + ``` + name: student-project + channels: + - conda-forge + dependencies: + - scipy=1.3.1 + - numpy=1.16.4 + - sympy=1.4 + - click=7.0 + - python=3.8 + - someproject=1.2.3 + - anotherproject=2.3.4 + ``` + ```` + + ````{group-tab} Python virtualenv + **A**: + You find a couple of library imports across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a `requirements.txt` file with: + ``` + scipy + numpy + sympy + click + python + git+https://github.com/someuser/someproject.git@master + git+https://github.com/anotheruser/anotherproject.git@master + ``` + + **D**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + git+https://github.com/someuser/someproject.git@d7b2c7e + git+https://github.com/anotheruser/anotherproject.git@sometag + ``` + + **E**: + You find a `requirements.txt` file with: + ``` + scipy==1.3.1 + numpy==1.16.4 + sympy==1.4 + click==7.0 + python==3.8 + someproject==1.2.3 + anotherproject==2.3.4 + ``` + ```` + + ````{group-tab} R + **A**: + You find a couple of `library()` or `require()` calls across the code but that's it. + + **B**: + The README file lists which libraries were used but does not mention + any versions. + + **C**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr, + tidyr + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@master") + remotes::install_github("anotheruser/anotherproject@master") + ``` + + **D**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0) + ``` + In addition you find these: + ```r + remotes::install_github("someuser/someproject@d7b2c7e") + remotes::install_github("anotheruser/anotherproject@sometag") + ``` + + **E**: + You find a [DESCRIPTION file](https://r-pkgs.org/description.html) which contains: + ``` + Imports: + dplyr (== 1.0.0), + tidyr (== 1.1.0), + someproject (== 1.2.3), + anotherproject (== 2.3.4) + ``` + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` + + `````{solution} + **A**: It will be tedious to collect the dependencies one by one. And after + the tedious process you will still not know which versions they have used. + + **B**: If there is no standard file to look for and look at and it might + become very difficult for to create the software environment required to + run the software. But at least we know the list of libraries. But we don't + know the versions. + + **C**: Having a standard file listing dependencies is definitely better + than nothing. However, if the versions are not specified, you or someone + else might run into problems with dependencies, deprecated features, + changes in package APIs, etc. + + **D** and **E**: In both these cases exact versions of all dependencies are + specified and one can recreate the software environment required for the + project. One problem with the dependencies that come from GitHub is that + they might have disappeared (what if their authors deleted these + repositories?). + + **E** is slightly preferable because version numbers are easier to understand than Git + commit hashes or Git tags. + ````` +`````` + +``````{challenge} (optional) Dependencies-2: Create a time-capsule for the future +Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information? + + `````{tabs} + ````{group-tab} Conda + Try this either with your own project or inside the "coderefinery" conda + environment: + ```console + $ conda env export > environment.yml + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ conda env create -f environment.yml + ``` + + More information: + + See also: + ```` + + ````{group-tab} Python virtualenv + Try this in your own project: + ```console + $ pip freeze > requirements.txt + ``` + + Have a look at the generated file and discuss what you see. + + In future you can re-create this environment with: + ```console + $ pip install -r requirements.txt + ``` + + More information: + ```` + + ````{group-tab} R + This example uses renv. + + Try to "save" and "load" the state of your project library using + `renv::snapshot()` and `renv::restore()`. + See also: + + More information: + ```` + + ````{group-tab} Matlab + Can you please contribute an example? + ```` + ````` +`````` diff --git a/branch/swi_snakemake/_sources/environments.md.txt b/branch/swi_snakemake/_sources/environments.md.txt new file mode 100644 index 0000000..386ae88 --- /dev/null +++ b/branch/swi_snakemake/_sources/environments.md.txt @@ -0,0 +1,280 @@ +# Recording environments + +```{objectives} +- Understand what containers are +- Understand good and less good usecases for containers +- Discuss container definitions files in the context of reusability and + reproducibility +``` + +```{instructor-note} +- 10 min teaching/discussion +- 20 min exercise +``` + + +## What is a container? + +Imagine if you didn't have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +**like an entire operating system with software installed, all in one file**, + +```{figure} img/docker_meme.jpg +:alt: He said, then we will ship your machine. And that's how Docker was born. +:width: 60% + +From [reddit](https://www.reddit.com/r/ProgrammerHumor/comments/cw58z7/it_works_on_my_machine/). +``` + +``````{discussion} Kitchen analogy +- Our codes/scripts <-> cooking recipes +- Container definition files <-> like a blueprint to build a kitchen with all + utensils in which the recipe can be prepared. +- Container images <-> example kitchens +- Containers <-> identical factory-built mobile food truck kitchens + +Just for fun: which operating systems do the following example kitchens represent? + `````{tabs} + ````{tab} 1 + ```{figure} img/kitchen/macos.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 2 + ```{figure} img/kitchen/windows.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + + ````{tab} 3 + ```{figure} img/kitchen/linux.png + :alt: Generated image of a kitchen + :width: 50% + + [Midjourney, CC-BY-NC 4.0] + ``` + ```` + ````` +`````` + + +## From definition files to container images to containers + +- Containers can be built to bundle *all the necessary ingredients* (data, code, environment, operating system). +- A container image is like a piece of paper with all the operating system on it. When you run it, + a transparent sheet is placed on top to form a container. The container runs and writes only on + that transparent sheet (and what other mounts have been layered on top). When you are done, + transparency is thrown away. It can be repeated as often as you want, and base is always the same. +- Definition files (e.g. Dockerfile or Singularity definition file) are text + files that contain a series of instructions to build container images. + +## You may have use for containers in different ways + +- Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead! +- You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container! + - If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough. + +## The container recipe + +Here is an example of a Singularity definition file ([reference](https://apptainer.org/docs/user/main/build_a_container.html#building-containers-from-apptainer-definition-files)): +``` +Bootstrap: docker +From: ubuntu:20.04 + +%post + apt-get -y update + apt-get -y install cowsay lolcat + +%environment + export LC_ALL=C + export PATH=/usr/games:$PATH + +%runscript + date | cowsay | lolcat +``` + +Popular container implementations: +- [Docker](https://www.docker.com/) +- [Singularity](https://sylabs.io/docs/) (popular on high-performance computing systems) +- [Apptainer](https://apptainer.org) (popular on high-performance computing systems, fork of Singularity) +- [podman](https://podman.io/) + +They are to some extent interoperable: +- podman is very close to Docker +- Docker images can be converted to Singularity/Apptainer images +- [Singularity Python](https://singularityhub.github.io/singularity-cli/) can convert Dockerfiles to Singularity definition files + +--- + +## Pros and cons of containers + +Containers are popular for a reason - they solve a number of +important problems: +- Allow for seamlessly moving workflows across different platforms. +- Can solve the "works on my machine" situation. +- For software with many dependencies, in turn with its own dependencies, + containers offer possibly the only way to preserve the + computational experiment for future reproducibility. +- A mechanism to "send the computer to the data" when data is too +- Installing software into a file instead of into your computer (removing + a file is often easier than uninstalling software if you suddenly regret an + installation) + +However, containers may also have some drawbacks: +- Can be used to hide away software installation problems and thereby + discourage good software development practices. +- Instead of "works on my machine" problem: "works only in this container" problem? +- They can be difficult to modify (this is the focus of an exercise below) +- Container images can become large + +```{danger} +Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories. +``` + +--- + +## Where can one share or find images? + +- [Docker Hub](https://hub.docker.com/) +- [Quay](https://quay.io/) +- [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) +- [GitLab Container Registry](https://docs.gitlab.com/ee/user/packages/container_registry/) +- GitHub/GitLab release artifacts +- [Zenodo](https://zenodo.org/) + +--- + +## Exercises + +``````{exercise} Containers-1: Time travel + Scenario: A researcher has written and published their research code which + requires a number of libraries and system dependencies. They ran their code + on a Linux computer (Ubuntu). One very nice thing they did was to publish + also a container image with all dependencies included, as well as the + definition file (below) to create the container image. + + Now we travel 3 years into the future and want to reuse their work and adapt + it for our data. The container registry where they uploaded the container + image however no longer exists. But luckily we still have the definition file + (below)! From this we should be able to create a new container image. + + - Can you anticipate problems using the definitions file 3 years after its creation? + Which possible problems can you point out? + - Discuss possible take-aways for creating more reusable containers. + + `````{tabs} + ````{tab} Python project using virtual environment + ```{code-block} + :linenos: + Bootstrap: docker + From: ubuntu:latest + + %post + # Set environment variables + export VIRTUAL_ENV=/app/venv + + # Install system dependencies and Python 3 + apt-get update && \ + apt-get install -y --no-install-recommends \ + gcc \ + libgomp1 \ + python3 \ + python3-venv \ + python3-distutils \ + python3-pip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + + # Set up the virtual environment + python3 -m venv $VIRTUAL_ENV + . $VIRTUAL_ENV/bin/activate + + # Install Python libraries + pip install --no-cache-dir --upgrade pip && \ + pip install --no-cache-dir -r /app/requirements.txt + + %files + # Copy project files + ./requirements.txt /app/requirements.txt + ./app.py /app/app.py + # Copy data + /home/myself/data /app/data + # Workaround to fix dependency on fancylib + /home/myself/fancylib /usr/lib/fancylib + + %environment + # Set the environment variables + export LANG=C.UTF-8 LC_ALL=C.UTF-8 + export VIRTUAL_ENV=/app/venv + + %runscript + # Activate the virtual environment + . $VIRTUAL_ENV/bin/activate + # Run the application + python /app/app.py + ``` + + ```{solution} + - Line 2: "ubuntu:latest" will mean something different 3 years in future. + - Lines 11-12: The compiler gcc and the library libgomp1 will have evolved. + - Line 30: The container uses requirements.txt to build the virtual environment but we don't see + here what libraries the code depends on. + - Line 33: Data is copied in from the hard disk of the person who created it. Hopefully we can find the data somewhere. + - Line 35: The library fancylib has been built outside the container and copied in but we don't see here how it was done. + - Python version will be different then and hopefully the code still runs then. + - Singularity/Apptainer will have also evolved by then. Hopefully this definition file then still works. + - No contact address to ask more questions about this file. + - (Can you find more? Please contribute more points.) + ``` + ```` + + ````{tab} R project using renv + Work in progress: Please contribute a corresponding example which + demonstrates this in the context of R and renv. + ```` + ````` +`````` + +````{exercise} (optional) Containers-2: Explore two really useful Docker images +You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer. + +1. Run a specific version of *Rstudio*: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio + ``` + + Then open your browser to [http://localhost:8787](http://localhost:8787) + with login rstudio and password "yourpasswordhere" used in the previous + command. + + If you want to try an older version you can check the tags at + [https://hub.docker.com/r/rocker/rstudio/tags](https://hub.docker.com/r/rocker/rstudio/tags) + and run for example: + ```console + $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3 + ``` + +2. Run a specific version of *Anaconda3* from + [https://hub.docker.com/r/continuumio/anaconda3](https://hub.docker.com/r/continuumio/anaconda3): + ```console + $ docker run -i -t continuumio/anaconda3 /bin/bash + ``` +```` + +## Resources for further learning + +- [Carpentries incubator lesson on Docker](https://carpentries-incubator.github.io/docker-introduction/) +- [Carpentries incubator lesson on Singularity/Apptainer](https://carpentries-incubator.github.io/singularity-introduction/) \ No newline at end of file diff --git a/branch/swi_snakemake/_sources/exercises.md.txt b/branch/swi_snakemake/_sources/exercises.md.txt new file mode 100644 index 0000000..61028b9 --- /dev/null +++ b/branch/swi_snakemake/_sources/exercises.md.txt @@ -0,0 +1,12 @@ +# List of exercises + +## Full list + +This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests. + +```{exerciselist} +``` diff --git a/branch/swi_snakemake/_sources/guide.md.txt b/branch/swi_snakemake/_sources/guide.md.txt new file mode 100644 index 0000000..97261f0 --- /dev/null +++ b/branch/swi_snakemake/_sources/guide.md.txt @@ -0,0 +1,155 @@ +--- +layout: default +permalink: /guide/ +--- + +# Instructor guide + + +## Detailed day schedule + +Two example schedules for this lesson: + +This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson: + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Overview of CR and how it all fits together +- 09:10 - 09:20 Reproducible research, [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:27 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:27 - 09:35 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) - discussion +- 09:35 - 10:00 Snakemake exercise (25 min) +- 10:00 - 10:10 Break +- 10:10 - 10:15 Summary of workflows and the exercise +- 10:15 - 10:30 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- 10:30 - 10:40 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) +- 10:40 - 11:00 Container-1 exercise (20 min) +- 11:00 - 11.05 Wrapup + +This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break): + +- 08:50 - 09:00 Soft start and icebreaker question +- 09:00 - 09:10 Interview with an invited guest +- 09:10 - 09:20 [Motivation](https://coderefinery.github.io/reproducible-research/motivation/) +- 09:20 - 09:30 [Organizing your projects](https://coderefinery.github.io/reproducible-research/organizing-projects/) +- 09:30 - 10:00 [Recording dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:00 - 10:10 Break +- 10:10 - 10:40 [Recording computational steps](https://coderefinery.github.io/reproducible-research/workflow-management/) + - discussion (5 min) + - exercise (20 min) + - discussion (5 min) +- 10:40 - 10:50 [Recording environments](https://coderefinery.github.io/reproducible-research/environments/) + - an exercise exists but is typically not done as part of a standard workshop +- 10:50 - 11:05 [Sharing code and data](https://coderefinery.github.io/reproducible-research/sharing/) + - [demo (15 min)](https://coderefinery.github.io/reproducible-research/sharing/#connecting-repositories-to-zenodo) +- 11:05 - 11:15 Break + + +## Why we teach this lesson + +Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey. + +Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility. + +Many participants may not adhere to good practices when organizing their projects, +and the "Organizing your projects" episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn't harm to preach to the choir. + +Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people's code to run), they +often don't know or use good practices when it comes to recording dependencies. +Most participants also don't use isolated environments for different projects and +don't know why that can be important. +The episode "Recording dependencies" tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager. + +Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +"Recording environments" introduces the concept of containers, and the optional +episode "Creating and sharing a container image" goes into details. + +Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of "scientific workflows", +and that there actually exist tools that help make such workflows reproducible. +The episode "Recording computational steps" introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible. + + +## How to teach this lesson + +### How to start + +Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we're going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers). + + +### Focus on concepts, and when to use which tool + +Try to explain better what the different tools are useful for, but don't go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem. + + +## Typical pitfalls + +### Indentation in Snakefiles + +- the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn't matter +This works: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +but this doesn't work: +```python +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` +nor this: +```python +rule all: +input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) +``` + + +## Field reports + +### 2022 September + +We used the strategy "absolutely minimal introductions, most time +for exercise". Overall, it was probably the right thing to do since +there is so little time and so much to cover. + +There wasn't enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode. + +The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn't really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day. + diff --git a/branch/swi_snakemake/_sources/index.rst.txt b/branch/swi_snakemake/_sources/index.rst.txt new file mode 100644 index 0000000..1af87bd --- /dev/null +++ b/branch/swi_snakemake/_sources/index.rst.txt @@ -0,0 +1,60 @@ +.. _index: + +Reproducible research - Preparing code to be usable by you and others in the future +=================================================================================== + +Have you ever spent days **trying to repeat the results from few weeks or months +ago**? Or you have to do paper revisions, but you just can't get the results to +match up? It's unpleasant for both you and science. + +In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to **record +reproducible environments and computational steps** for our future selves. + + +.. admonition:: Learning outcomes + + By the end of this lesson, learners should: + - be able to apply well organized directory structure for their project + - remember the FAIR principles + - understand that code can have dependencies, and know how to document them + - if a computational studies contains several steps, be able to document them + - know about use cases for containers + - knowing the pros and cons of manual documentation vs. scripted automation vs. workflow management + + +.. prereq:: + + You need to install + `Git, Python, and Snakemake `__. + + +.. toctree:: + :maxdepth: 1 + :caption: Core episodes + + intro.md + motivation.md + organizing-projects.md + workflow-management.md + dependencies.md + environments.md + where-to-go.md + + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + exercises + guide + + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + CodeRefinery + Reusing diff --git a/branch/swi_snakemake/_sources/intro.md.txt b/branch/swi_snakemake/_sources/intro.md.txt new file mode 100644 index 0000000..6690f38 --- /dev/null +++ b/branch/swi_snakemake/_sources/intro.md.txt @@ -0,0 +1,16 @@ +# Introduction - How it all connects + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +--- + +```{figure} img/reproducible_research_plus_lessons.png +:alt: "6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0" +:width: 100% +``` + +[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, ] + diff --git a/branch/swi_snakemake/_sources/motivation.md.txt b/branch/swi_snakemake/_sources/motivation.md.txt new file mode 100644 index 0000000..a55220a --- /dev/null +++ b/branch/swi_snakemake/_sources/motivation.md.txt @@ -0,0 +1,71 @@ +# Motivation + +```{instructor-note} +- 10 min teaching/discussion +- 0 min exercises +``` + +```{figure} img/research_comic_phd.gif +:alt: Research comic +:width: 100% +``` + +```{admonition} A scary anecdote +- A group of researchers obtain great results and submit their work to a high-profile journal. +- Reviewers ask for new figures and additional analysis. +- The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures. +- The researchers can't find some of the data they used to generate the original results, and + can't figure out which parameters they used when running their analyses. +- The manuscript is still languishing in the drawer ... +``` + +--- + +## Why talking about reproducible research? + +A 2016 +[survey](http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970) +in Nature revealed that irreproducible experiments are a problem across all +domains of science: + +```{figure} img/reproducibility_nature.jpg +:alt: reproduciblity Nature +:width: 100% +``` + +This study is now few years old but the highlighted problem did not get +smaller. + +--- + +## Levels of reproducibility + +A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility. + +```{figure} img/repro-pyramid.png +:alt: Reproducibility pyramid +:width: 100% +``` + +[Steeves, Vicky (2017) in "Reproducibility Librarianship," Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4] + +This also means that you can think about it from the beginning of your research life cycle! + +--- + +````{discussion} Discuss in collaborative document or with your team members +```markdown +- What are your experiences re-running or adjusting a script or a figure you + created few months ago? + - ... + - ... + - (share your experience) + +- Have you continued working from a previous student's + script/code/plot/notebook? What were the biggest challenges? + - ... + - ... + - (share your experience, but constructively) +```` diff --git a/branch/swi_snakemake/_sources/organizing-projects.md.txt b/branch/swi_snakemake/_sources/organizing-projects.md.txt new file mode 100644 index 0000000..9b8e04a --- /dev/null +++ b/branch/swi_snakemake/_sources/organizing-projects.md.txt @@ -0,0 +1,125 @@ +# Organizing your projects + +```{objectives} +- Get an overview on how to organize research projects +``` + +```{instructor-note} +- 10 min teaching incl. discussions +``` + +One of the most basic steps to make your work reproducible is to organize your projects well. +Let's go over some of the basic things which people have found to work (and not to work). + + +## Directory structure for projects + +- Project files in a **single folder** +- **Different projects** should have **separate folders** +- Use **consistent and informative directory structure** + - Avoid spaces in directory and file names – it is uglier for humans but handy for computers. +- If you need to separate public/private, you can put them in public and private Git repos + - If you need to separate public/secret, use `.gitignore` or a separate folder that's not in Git +- Add a **README file** to describe the project and instructions on reproducing the results +- If a software is reused in several projects it can make sense to put them in own repo + +A project directory can look something like this: +```shell +project_name/ +├── README.md # overview of the project +├── data/ # data files used in the project +│ ├── README.md # describes where data came from +│ └── sub-folder/ # may contain subdirectories +├── processed_data/ # intermediate files from the analysis +├── manuscript/ # manuscript describing the results +├── results/ # results of the analysis (data, tables, figures) +├── src/ # contains all code in the project +│ ├── LICENSE # license for your code +│ ├── requirements.txt # software requirements and dependencies +│ └── ... +└── doc/ # documentation for your project + ├── index.rst + └── ... +``` +--- + +## Tracking source code, data, and results + +- All code is version controlled and goes in the `src/` or `source/` directory +- Include appropriate LICENSE file and information on software requirements +- You can also version control data files or input files under `data/` +- If data files are too large (or sensitive) to track, untrack them using `.gitignore` +- Intermediate files from the analysis are kept in `processed_data/` +- Consider using Git tags to mark specific versions of results (version + submitted to a journal, dissertation version, poster version, etc.): + ```console + $ git tag -a thesis-submitted -m "this is the submitted version of my thesis" + ``` +* Check the [Git-intro lesson](https://coderefinery.github.io/git-intro/) for a reminder. + +--- + +## Reproducible publications + +- Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist: + - [Overleaf](https://www.overleaf.com): an online, collaborative LaTeX editor (has Git integration) + - [Authorea](https://www.authorea.com): collaborative platform for preprints (apparently also has Git integration) + - [HackMD](https://hackmd.io/): an online collaborative Markdown editor (has Git integration) + - [Manuscripts.io](https://www.manuscripts.io/): a collaborative authoring tool that support scientific content and reproducibility. + - Google Docs can be a good alternative + +- Many tools exist to assist in making scholarly output reproducible: + - [rrtools](https://github.com/benmarwick/rrtools): instructions, templates, and functions for writing a reproducible article or report with R. + - [Jupyter Notebooks](https://jupyter.org): web-based computational environment for creating code and text based notebooks that can be used as, see also our [Jupyter lesson](https://coderefinery.github.io/jupyter/) later in this workshop. + supplementary material for articles. + - [Binder](https://mybinder.org): makes a repository with Jupyter notebooks available in an executable environment (discussed later in the [Jupyter lesson](https://coderefinery.github.io/jupyter/)). + - ["Research compendia"](http://inundata.org/talks/rstd19/#/): a set of good practices for + reproducible data analysis in R, but much is transferable to other languages. + +```{seealso} +Do you want to practice your reproducibility skills and get inspired by working with other people's code/data? Join a [ReproHack event](https://www.reprohack.org/event/)! +``` + + +--- + +## Discussion on reproducibility + +````{discussion} Discuss in collaborative document or with your team members +**How do you collaborate on writing academic papers?** +``` +- Are you using version control for academic papers? + - ... + - ... + - (share your experience) + +- How do you handle collaborative issues e.g. conflicting changes? + - ... + - ... + - (share your experience) +``` +> Please write or discuss your ideas before opening solution! + +```{solution} +- Consider using version control for manuscripts as well. It may help you when keeping track of edits + if you sync it online then you don't have to worry about losing your work. + +- Collaboration can be done efficiently by + - real time collaboration tools like HackMD/HedgeDoc where conflicts are resolved on the fly + - version control where conflicts are detected and shown – and solved manually +``` +```` + +````{discussion} Discuss in collaborative document or with your team members +``` +- What tools are you using when organizing your projects? + - ... + - ... + - (share your experience) +``` +```` + + +```{keypoints} +- An organized project directory structure helps with reproducibility. +- Reproducibility makes work easier for the next person working on the project - and that might be you in a few years! +``` diff --git a/branch/swi_snakemake/_sources/where-to-go.md.txt b/branch/swi_snakemake/_sources/where-to-go.md.txt new file mode 100644 index 0000000..9c49f32 --- /dev/null +++ b/branch/swi_snakemake/_sources/where-to-go.md.txt @@ -0,0 +1,50 @@ +# Where to go from here + +```{objectives} +- Understand when tools discussed in this episode can be useful +``` + +```{instructor-note} +- 10 min teaching/discussion +``` + +This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project. + +## Important for every project + +* Clear file structure for your project +* At least consider the possibility that someone, maybe you may want to reproduce your work + * Can you do something (small) to make it easier? + * If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help. + +## Workflow tools will maybe make sense in the future + +* In many cases, it is probably not needed +* You will want to consider workflow tools: + * When processing many files with many steps + * Steps or files may change + * Your main script, connecting your steps gets very long + * ... + +## When should I worry about dependencies? + +* Your code depends on multiple other packages +* You want to avoid questions like: "What do I need to install to run your code" +* You want help yourself running your code + * After a few years + * On a different computer + * ... + +## Containers seem amazing, but do I have use for them? + +* Maybe not yet, but knowing that you can ... + * Run Linux tools on your Windows computer + * Run different versions of same software on your computer + * Follow the "easy installation instructions" for an operating system that is not your own + * Get a fully configured environment instead of only installing a tool + * Share your setup and configurations with others +... can be very beneficial :) + + + diff --git a/branch/swi_snakemake/_sources/workflow-management.md.txt b/branch/swi_snakemake/_sources/workflow-management.md.txt new file mode 100644 index 0000000..8909516 --- /dev/null +++ b/branch/swi_snakemake/_sources/workflow-management.md.txt @@ -0,0 +1,236 @@ +# Recording computational steps + +```{questions} +- You have some steps that need to be run to do your work. How do you + actually run them? Does it rely on your own memory and work, or is it + reproducible? **How do you communicate the steps** for future you and others? +- How can we create a reproducible workflow? +- When to use scientific workflow management systems. +``` + +```{instructor-note} +- 5 min teaching +- 15 min demo +``` + + +## Several steps from input data to result + +*The following material is partly derived from a [HPC Carpentry lesson](https://hpc-carpentry.github.io/hpc-python/).* + +In this episode, we will use an [example +project](https://github.com/coderefinery/word-count) which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to: + +1. Analyze word frequencies using [statistics/count.py](https://github.com/coderefinery/word-count/blob/main/statistics/count.py) + for 4 books + (they are all in the [data](https://github.com/coderefinery/word-count/tree/main/data) directory). +2. Plot a histogram using [plot/plot.py](https://github.com/coderefinery/word-count/blob/main/plot/plot.py). + +```{figure} img/word-count/arrows.png +:alt: From book to word counts to plot +:width: 100% +``` + +Example (for one book only): + +```console +$ python statistics/count.py data/isles.txt > statistics/isles.data +$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png +``` + +Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps. + +Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But **imagine having 4 steps and 500 books**. +How could we deal with this? + +As a first idea we could express the workflow with a script. The repository includes such script called `run_all.sh`. + +We can run it with: + +```console +$ bash run_all.sh +``` + +This is **imperative style**: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another. + +````{discussion} +- What are the advantages of this solution compared to processing all one by one? +- Is the scripted solution reproducible? +- Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate + with a scripted solution? + + ```{solution} + The advantage of this solution compared to processing one by one is more automation: We can generate all. + This is not only easier, it is also less error-prone. + + Yes, the scripted solution can be reproducible. But could you easily run it e.g. on a Windows computer? + + If we had more steps and once steps start to be time-consuming, a limitation of + a scripted solution is that it tries to run all steps always. Rerunning only + part of the steps or only part of the input data requires us to outcomment or change lines in our script in between runs which can again become tedious and error-prone. + ``` +```` + +--- + +## Workflow tools + +Sometimes it may be helpful to go from imperative to declarative style. Rather than saying "do this and then that" we describe dependencies but we let the tool figure out the series of steps to produce results. + +### Example workflow tool: [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) + +Snakemake (inspired by [GNU Make](https://www.gnu.org/software/make/)) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition. + +--- + +## A demo + +````{prereq} Preparation +The exercise (below) and pre-exercise discussion uses the +word-count repository +() which we need to clone to work on it. + +If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the [CodeRefinery installation instruction page](https://coderefinery.github.io/installation/)), or the [Binder](https://mybinder.org/) +cloud service: + +**On your own computer**: +- Install the necessary tools +- Activate the [coderefinery conda environment](https://coderefinery.github.io/installation/conda-environment/) with `conda activate coderefinery`. +- Clone the word-count repository: + ```console + $ git clone https://github.com/coderefinery/word-count.git + ``` + +**On Binder**: +We can also use the cloud service [Binder](https://mybinder.org/) to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it's explained further in the [Jupyter +lesson](https://coderefinery.github.io/jupyter/sharing/) how this is even +possible. +- Go to and click on the "launch binder" badge in the README. +- Once it get started, you can open a new Terminal from the **new** menu (top right) and select **Terminal**. +```` + +````{exercise} Workflow-1: Workflow solution using Snakemake + +```{figure} img/snakemake.png +:alt: How Snakemake works +:width: 100% +``` + +Somebody wrote a [Snakemake](https://snakemake.readthedocs.io) solution in the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile): +``` +# a list of all the books we are analyzing +DATA = glob_wildcards('data/{book}.txt').book + +rule all: + input: + expand('statistics/{book}.data', book=DATA), + expand('plot/{book}.png', book=DATA) + +# count words in one of our books +rule count_words: + input: + script='code/count.py', + book='data/{file}.txt' + output: 'statistics/{file}.data' + shell: 'python {input.script} {input.book} > {output}' + +# create a plot for each book +rule make_plot: + input: + script='code/plot.py', + book='statistics/{file}.data' + output: 'plot/{file}.png' + shell: 'python {input.script} --data-file {input.book} --plot-file {output}' + +``` + +We can see that Snakemake uses **declarative style**: +Snakefiles contain rules that relate targets (`output`) to dependencies +(`input`) and commands (`shell`). + +Steps: +1. Clone the example to your computer: `$ git clone https://github.com/coderefinery/word-count.git` +2. Study the Snakefile. How does it know what to do first and what to do then? +3. Try to run it. Since version 5.11 one needs to specify number of cores (or + jobs) using `-j`, `--jobs` or `--cores`: + ```console + $ snakemake --delete-all-output -j 1 + $ snakemake -j 1 + ``` + The `--delete-all-output` part makes sure that we remove all generated files before we start. +4. Try running `snakemake` again and observe that and discuss why it refused to rerun all steps: + ```console + $ snakemake -j 1 + + Building DAG of jobs... + Nothing to be done (all requested files are present and up to date). + ``` +5. Make a tiny modification to the plot.py script and run `$ snakemake -j 1` again and observe how it will only re-run the plot steps. +6. Make a tiny modification to one of the books and run `$ snakemake -j 1` again and observe how it only regenerates files for this book. +7. Discuss possible advantages compared to a scripted solution. +8. **Question for R developers**: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in + the [Snakefile](https://github.com/coderefinery/word-count/blob/main/Snakefile) would you have to modify so that it uses your R code? +9. If you make changes to the Snakefile, validate it using `$ snakemake --lint`. + +```{solution} +- 2: Start with "all" and look what it depends on. Now search for rules that + have these as output. Look for their inputs and search where they + are produced. In other words, search backwards and build a graph of + dependencies. This is what Snakemake does. +- 4: It can see that outputs are newer than inputs. It will only regenerate + outputs if they are not there or if the inputs or scripts have changed. +- 7: It only generates steps and outputs that are missing or outdated. The workflow + does not run everything every time. In other words if you notice a problem or update information + "half way" in the analysis, it will only re-run what needs to be re-run. Nothing more, nothing less. + Another advantage is that it can distribute tasks to multiple cores, off-load work to supercomputers, + offers more fine-grained control over environments, and more. +- 8: Probably only the two lines containing "shell". +``` +```` + +## Visualizing the workflow + +We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the `--dag` option, which will output the DAG in `dot` language. + +**Note**: This requires the [Graphviz software](https://www.graphviz.org/), +which can be installed by `conda install graphviz`. + +```console +$ snakemake -j 1 --dag | dot -Tpng > dag.png +``` +Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines. + +```{figure} img/snakemake_dag.png +:alt: Snakemake DAG +:width: 100% +``` + +## Why [Snakemake](https://snakemake.readthedocs.io/)? + +- Gentle **learning curve**. +- Free, open-source, and **installs easily** via conda or pip. +- **Cross-platform** (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: + same workflow works without modification and scales appropriately whether on a laptop or cluster. +- If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them **in parallel**. +- Is is possible to define **isolated software environments** per rule, e.g. by adding `conda: 'environment.yml'` to a rule. +- Also possible to run workflows in Docker or Apptainer **containers** e.g. by adding `container: 'docker://some-org/some-tool#2.3.1'` to a rule. +- [Heavily used in bioinformatics](https://twitter.com/carl_witt/status/1103951128046301185), but is **completely general**. +- Nice functionality for archiving the workflow, see: [the official documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#sustainable-and-reproducible-archiving) + +Tools like Snakemake help us with **reproducibility** by supporting us with **automation**, **scalability** and **portability** of our workflows. + +## Similar tools + +- [Make](https://www.gnu.org/software/make/) +- [Nextflow](https://www.nextflow.io/) +- [Task](https://taskfile.dev/) +- [Common Workflow Language](https://www.commonwl.org/) +- Many [specialized frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) exist. +- [Book on building reproducible analytical pipelines with R](https://raps-with-r.dev/) diff --git a/branch/swi_snakemake/_static/_sphinx_javascript_frameworks_compat.js b/branch/swi_snakemake/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/swi_snakemake/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_snakemake/_static/check-solid.svg b/branch/swi_snakemake/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/swi_snakemake/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/swi_snakemake/_static/clipboard.min.js b/branch/swi_snakemake/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/swi_snakemake/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/swi_snakemake/_static/copybutton.css b/branch/swi_snakemake/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/swi_snakemake/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/swi_snakemake/_static/copybutton.js b/branch/swi_snakemake/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/swi_snakemake/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/swi_snakemake/_static/copybutton_funcs.js b/branch/swi_snakemake/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/swi_snakemake/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + 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+} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight 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details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/swi_snakemake/_static/sphinx_highlight.js b/branch/swi_snakemake/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/swi_snakemake/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/swi_snakemake/_static/sphinx_lesson.css b/branch/swi_snakemake/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/swi_snakemake/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/swi_snakemake/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/swi_snakemake/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/swi_snakemake/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/swi_snakemake/_static/tabs.css b/branch/swi_snakemake/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/swi_snakemake/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/swi_snakemake/_static/tabs.js b/branch/swi_snakemake/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/swi_snakemake/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/swi_snakemake/_static/term_role_formatting.css b/branch/swi_snakemake/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/swi_snakemake/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/swi_snakemake/_static/togglebutton.css b/branch/swi_snakemake/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/swi_snakemake/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_snakemake/_static/togglebutton.js b/branch/swi_snakemake/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/swi_snakemake/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/swi_snakemake/dependencies/index.html b/branch/swi_snakemake/dependencies/index.html new file mode 100644 index 0000000..a5fd513 --- /dev/null +++ b/branch/swi_snakemake/dependencies/index.html @@ -0,0 +1,426 @@ + + + + + + + Recording dependencies — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 20 min exercises

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing a mess of dependecies in a Python environment +
+

From xkcd.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Exercises

+
+

(optional) Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

(optional) Dependencies-2: Create a time-capsule for the future

+

Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/environments/index.html b/branch/swi_snakemake/environments/index.html new file mode 100644 index 0000000..b288a18 --- /dev/null +++ b/branch/swi_snakemake/environments/index.html @@ -0,0 +1,438 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 20 min exercise

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file,

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/exercises/index.html b/branch/swi_snakemake/exercises/index.html new file mode 100644 index 0000000..bf7a36b --- /dev/null +++ b/branch/swi_snakemake/exercises/index.html @@ -0,0 +1,629 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording computational steps

+

In workflow-management.md:

+ +

In workflow-management.md:

+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording dependencies

+

In dependencies.md:

+
+

(optional) Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

(optional) Dependencies-2: Create a time-capsule for the future

+

Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/genindex/index.html b/branch/swi_snakemake/genindex/index.html new file mode 100644 index 0000000..040ed0f --- /dev/null +++ b/branch/swi_snakemake/genindex/index.html @@ -0,0 +1,143 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/guide/index.html b/branch/swi_snakemake/guide/index.html new file mode 100644 index 0000000..3ba180b --- /dev/null +++ b/branch/swi_snakemake/guide/index.html @@ -0,0 +1,312 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/index.html b/branch/swi_snakemake/index.html new file mode 100644 index 0000000..8f3b557 --- /dev/null +++ b/branch/swi_snakemake/index.html @@ -0,0 +1,196 @@ + + + + + + + Reproducible research - Preparing code to be usable by you and others in the future — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research - Preparing code to be usable by you and others in the future
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • be able to apply well organized directory structure for their project

    • +

  • remember the FAIR principles

    • +

  • understand that code can have dependencies, and know how to document them

    • +

  • if a computational studies contains several steps, be able to document them

    • +

  • know about use cases for containers

    • +

  • knowing the pros and cons of manual documentation vs. scripted automation vs. workflow management

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/intro/index.html b/branch/swi_snakemake/intro/index.html new file mode 100644 index 0000000..14bc998 --- /dev/null +++ b/branch/swi_snakemake/intro/index.html @@ -0,0 +1,157 @@ + + + + + + + Introduction - How it all connects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/lesson.pdf b/branch/swi_snakemake/lesson.pdf new file mode 100644 index 0000000..f759e5e Binary files /dev/null and b/branch/swi_snakemake/lesson.pdf differ diff --git a/branch/swi_snakemake/motivation/index.html b/branch/swi_snakemake/motivation/index.html new file mode 100644 index 0000000..dccc42a --- /dev/null +++ b/branch/swi_snakemake/motivation/index.html @@ -0,0 +1,212 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
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+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/objects.inv b/branch/swi_snakemake/objects.inv new file mode 100644 index 0000000..e482281 Binary files /dev/null and b/branch/swi_snakemake/objects.inv differ diff --git a/branch/swi_snakemake/organizing-projects/index.html b/branch/swi_snakemake/organizing-projects/index.html new file mode 100644 index 0000000..b0d6a57 --- /dev/null +++ b/branch/swi_snakemake/organizing-projects/index.html @@ -0,0 +1,301 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Organizing your projects

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Objectives

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  • Get an overview on how to organize research projects

    • +
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+

Instructor note

+
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  • 10 min teaching incl. discussions

    • +
+
+

One of the most basic steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
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  • Project files in a single folder

    • +

  • Different projects should have separate folders

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  • Use consistent and informative directory structure

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      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

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      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
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+

Tracking source code, data, and results

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  • All code is version controlled and goes in the src/ or source/ directory

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  • Include appropriate LICENSE file and information on software requirements

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  • You can also version control data files or input files under data/

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  • If data files are too large (or sensitive) to track, untrack them using .gitignore

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  • Intermediate files from the analysis are kept in processed_data/

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  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
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Reproducible publications

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  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist:

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    • Overleaf: an online, collaborative LaTeX editor (has Git integration)

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    • Authorea: collaborative platform for preprints (apparently also has Git integration)

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    • HackMD: an online collaborative Markdown editor (has Git integration)

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    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

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    • Google Docs can be a good alternative

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  • Many tools exist to assist in making scholarly output reproducible:

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    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

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    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

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    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

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    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

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See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

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+

Discussion on reproducibility

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+

Discuss in collaborative document or with your team members

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
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+

Please write or discuss your ideas before opening solution!

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+ +
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+

Discuss in collaborative document or with your team members

+
- What tools are you using when organizing your projects?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
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+

Keypoints

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  • An organized project directory structure helps with reproducibility.

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  • Reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

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+ + + + + + + + + \ No newline at end of file diff --git a/branch/swi_snakemake/searchindex.js b/branch/swi_snakemake/searchindex.js new file mode 100644 index 0000000..20f6e46 --- /dev/null +++ b/branch/swi_snakemake/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["dependencies", "environments", "exercises", "guide", "index", "intro", "motivation", "organizing-projects", "where-to-go", "workflow-management"], "filenames": ["dependencies.md", "environments.md", "exercises.md", "guide.md", "index.rst", "intro.md", "motivation.md", "organizing-projects.md", "where-to-go.md", "workflow-management.md"], "titles": ["Recording dependencies", "Recording environments", "List of exercises", "Instructor guide", "Reproducible research - Preparing code to be usable by you and others in the future", "Introduction - How it all connects", "Motivation", "Organizing your projects", "Where to go from here", "Recording computational steps"], "terms": {"how": [0, 1, 2, 4, 7, 9], "can": [0, 2, 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+}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/swi_snakemake/singlehtml/_static/basic.css b/branch/swi_snakemake/singlehtml/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_snakemake/singlehtml/_static/check-solid.svg b/branch/swi_snakemake/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/swi_snakemake/singlehtml/_static/clipboard.min.js b/branch/swi_snakemake/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/swi_snakemake/singlehtml/_static/copybutton.css b/branch/swi_snakemake/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/swi_snakemake/singlehtml/_static/copybutton.js b/branch/swi_snakemake/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/swi_snakemake/singlehtml/_static/copybutton_funcs.js b/branch/swi_snakemake/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/swi_snakemake/singlehtml/_static/css/badge_only.css b/branch/swi_snakemake/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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+ stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/branch/swi_snakemake/singlehtml/_static/minipres.js b/branch/swi_snakemake/singlehtml/_static/minipres.js new file mode 100644 index 0000000..ad11c87 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/minipres.js @@ -0,0 +1,223 @@ +// Add goTo method to elements +// http://stackoverflow.com/questions/4801655/how-to-go-to-a-specific-element-on-page +(function($) { + $.fn.goTo = function() { + $('html, body').animate({ + scrollTop: $(this).offset().top //+ 'px' + }, 'fast'); + return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + 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background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + 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background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight 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background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight 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.-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/swi_snakemake/singlehtml/_static/plus.png b/branch/swi_snakemake/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/swi_snakemake/singlehtml/_static/plus.png differ diff --git a/branch/swi_snakemake/singlehtml/_static/pygments.css b/branch/swi_snakemake/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: 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{ color: #666666 } /* Literal.Number.Bin */ +.highlight .mf { color: #666666 } /* Literal.Number.Float */ +.highlight .mh { color: #666666 } /* Literal.Number.Hex */ +.highlight .mi { color: #666666 } /* Literal.Number.Integer */ +.highlight .mo { color: #666666 } /* Literal.Number.Oct */ +.highlight .sa { color: #BA2121 } /* Literal.String.Affix */ +.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */ +.highlight .sc { color: #BA2121 } /* Literal.String.Char */ +.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */ +.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #BA2121 } /* Literal.String.Double */ +.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/swi_snakemake/singlehtml/_static/searchtools.js b/branch/swi_snakemake/singlehtml/_static/searchtools.js new file mode 100644 index 0000000..7918c3f --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/swi_snakemake/singlehtml/_static/sphinx_highlight.js b/branch/swi_snakemake/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/swi_snakemake/singlehtml/_static/sphinx_lesson.css b/branch/swi_snakemake/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/swi_snakemake/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/swi_snakemake/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/swi_snakemake/singlehtml/_static/tabs.css b/branch/swi_snakemake/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/swi_snakemake/singlehtml/_static/tabs.js b/branch/swi_snakemake/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/swi_snakemake/singlehtml/_static/term_role_formatting.css b/branch/swi_snakemake/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/swi_snakemake/singlehtml/_static/togglebutton.css b/branch/swi_snakemake/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/swi_snakemake/singlehtml/_static/togglebutton.js b/branch/swi_snakemake/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/swi_snakemake/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/swi_snakemake/singlehtml/index.html b/branch/swi_snakemake/singlehtml/index.html new file mode 100644 index 0000000..e59433a --- /dev/null +++ b/branch/swi_snakemake/singlehtml/index.html @@ -0,0 +1,1435 @@ + + + + + + + Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • be able to apply well organized directory structure for their project

    • +

  • remember the FAIR principles

    • +

  • understand that code can have dependencies, and know how to document them

    • +

  • if a computational studies contains several steps, be able to document them

    • +

  • know about use cases for containers

    • +

  • knowing the pros and cons of manual documentation vs. scripted automation vs. workflow management

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+
+
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the most basic steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist:

    +
      +

    • Overleaf: an online, collaborative LaTeX editor (has Git integration)

      • +

    • Authorea: collaborative platform for preprints (apparently also has Git integration)

      • +

    • HackMD: an online collaborative Markdown editor (has Git integration)

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+
+
+

Discussion on reproducibility

+
+

Discuss in collaborative document or with your team members

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+

Discuss in collaborative document or with your team members

+
- What tools are you using when organizing your projects?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +

  • Reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+
+
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 20 min exercises

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing a mess of dependecies in a Python environment +
+

From xkcd.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Exercises

+
+

(optional) Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

(optional) Dependencies-2: Create a time-capsule for the future

+

Now it is time to create your own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 20 min exercise

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file,

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+
+
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+
+
+
+
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+
+
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/singlehtml/objects.inv b/branch/swi_snakemake/singlehtml/objects.inv new file mode 100644 index 0000000..e7c16bd Binary files /dev/null and b/branch/swi_snakemake/singlehtml/objects.inv differ diff --git a/branch/swi_snakemake/where-to-go/index.html b/branch/swi_snakemake/where-to-go/index.html new file mode 100644 index 0000000..46745e1 --- /dev/null +++ b/branch/swi_snakemake/where-to-go/index.html @@ -0,0 +1,220 @@ + + + + + + + Where to go from here — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/swi_snakemake/workflow-management/index.html b/branch/swi_snakemake/workflow-management/index.html new file mode 100644 index 0000000..d9c4779 --- /dev/null +++ b/branch/swi_snakemake/workflow-management/index.html @@ -0,0 +1,386 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/dependencies/index.html b/dependencies/index.html new file mode 100644 index 0000000..1965948 --- /dev/null +++ b/dependencies/index.html @@ -0,0 +1,434 @@ + + + + + + + Recording dependencies — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/environments/index.html b/environments/index.html new file mode 100644 index 0000000..c70062f --- /dev/null +++ b/environments/index.html @@ -0,0 +1,446 @@ + + + + + + + Recording environments — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/exercises/index.html b/exercises/index.html new file mode 100644 index 0000000..b0faf96 --- /dev/null +++ b/exercises/index.html @@ -0,0 +1,630 @@ + + + + + + + List of exercises — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+

Organizing your projects

+

In organizing-projects.md:

+ +
+
+

Recording computational steps

+

In workflow-management.md:

+ +

In workflow-management.md:

+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Recording dependencies

+

In dependencies.md:

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+

In dependencies.md:

+ +

In dependencies.md:

+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+
+

Recording environments

+

In environments.md:

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+

In environments.md:

+ +

In environments.md:

+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex/index.html b/genindex/index.html new file mode 100644 index 0000000..3bacb50 --- /dev/null +++ b/genindex/index.html @@ -0,0 +1,144 @@ + + + + + + Index — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/guide/index.html b/guide/index.html new file mode 100644 index 0000000..859e3fe --- /dev/null +++ b/guide/index.html @@ -0,0 +1,313 @@ + + + + + + + Instructor guide — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..f49fd57 --- /dev/null +++ b/index.html @@ -0,0 +1,195 @@ + + + + + + + Reproducible research - Preparing code to be usable by you and others in the future — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research - Preparing code to be usable by you and others in the future
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+

Core episodes

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/intro/index.html b/intro/index.html new file mode 100644 index 0000000..c019e21 --- /dev/null +++ b/intro/index.html @@ -0,0 +1,158 @@ + + + + + + + Introduction - How it all connects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lesson.pdf b/lesson.pdf new file mode 100644 index 0000000..06413f9 Binary files /dev/null and b/lesson.pdf differ diff --git a/motivation/index.html b/motivation/index.html new file mode 100644 index 0000000..a6a7cf9 --- /dev/null +++ b/motivation/index.html @@ -0,0 +1,218 @@ + + + + + + + Motivation — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..e482281 Binary files /dev/null and b/objects.inv differ diff --git a/organizing-projects/index.html b/organizing-projects/index.html new file mode 100644 index 0000000..c74ad78 --- /dev/null +++ b/organizing-projects/index.html @@ -0,0 +1,301 @@ + + + + + + + Organizing your projects — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

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Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

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Keypoints

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  • An organized project directory structure helps with reproducibility.

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+} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/singlehtml/_static/check-solid.svg b/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/singlehtml/_static/clipboard.min.js b/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/singlehtml/_static/copybutton.css b/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/singlehtml/_static/copybutton.js b/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/singlehtml/_static/copybutton_funcs.js b/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/singlehtml/_static/css/badge_only.css b/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/singlehtml/_static/css/badge_only.css @@ -0,0 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+} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight 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(typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/singlehtml/_static/sphinx_highlight.js b/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/singlehtml/_static/sphinx_lesson.css b/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/singlehtml/_static/tabs.css b/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/singlehtml/_static/tabs.js b/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/singlehtml/_static/term_role_formatting.css b/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/singlehtml/_static/togglebutton.css b/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/singlehtml/_static/togglebutton.js b/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/singlehtml/index.html b/singlehtml/index.html new file mode 100644 index 0000000..4c9128f --- /dev/null +++ b/singlehtml/index.html @@ -0,0 +1,1465 @@ + + + + + + + Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reproducible research - Preparing code to be usable by you and others in the future

+

Have you ever spent days trying to repeat the results from few weeks or months +ago? Or you have to do paper revisions, but you just can’t get the results to +match up? It’s unpleasant for both you and science.

+

In this lesson we will explore different methods and tools for better +reproducibility in research software and data. We will demonstrate how version +control, workflows, containers, and package managers can be used to record +reproducible environments and computational steps for our future selves and others.

+
+

Learning outcomes

+
+
By the end of this lesson, learners should:
    +

  • Be able to apply well organized directory structure for their project

    • +

  • Understand that code can have dependencies, and know how to document them

    • +

  • Be able to document computational steps, and have an idea when it can be useful

    • +

  • Know about use cases for containers

    • +
+
+
+
+
+

Prerequisites

+

You need to install +Git, Python, and Snakemake.

+
+
+
+

Introduction - How it all connects

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 0 min exercises

    • +
+
+
+
+6 helpful steps for reproducible research: file organization, naming, documentation, version control, stabilizing computing environment, publishing research outputs, each step is connected to one or more CodeRefinery lesson - original figure (without lesson titles) by Heidi Seibold, CC-BY 4.0 +
+

[Adapted from original Figure by Heidi Seibold, CC-BY 4.0, https://twitter.com/HeidiBaya/status/1579385587865649153]

+
+
+

Motivation

+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+
+Research comic +
+
+

A scary anecdote

+
    +

  • A group of researchers obtain great results and submit their work to a high-profile journal.

    • +

  • Reviewers ask for new figures and additional analysis.

    • +

  • The researchers start working on revisions and generate modified figures, but find inconsistencies with old figures.

    • +

  • The researchers can’t find some of the data they used to generate the original results, and +can’t figure out which parameters they used when running their analyses.

    • +

  • The manuscript is still languishing in the drawer …

    • +
+
+
+
+

Why talking about reproducible research?

+

A 2016 +survey +in Nature revealed that irreproducible experiments are a problem across all +domains of science:

+
+reproduciblity Nature +
+

This study is now few years old but the highlighted problem did not get +smaller.

+
+
+
+

Levels of reproducibility

+

A published article is like the top of a pyramid. It rests on multiple +levels that each contributes to its reproducibility.

+
+Reproducibility pyramid +
+

[Steeves, Vicky (2017) in “Reproducibility Librarianship,” Collaborative Librarianship: Vol. 9: Iss. 2, Article 4. +Available at: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4]

+

This also means that you can think about it from the beginning of your research life cycle!

+
+
+

Discuss in collaborative document or with your team members

+
- What are your experiences re-running or adjusting a script or a figure you
+  created few months ago?
+  - ...
+  - ...
+  - (share your experience)
+
+- Have you continued working from a previous student's
+  script/code/plot/notebook? What were the biggest challenges?
+  - ...
+  - ...
+  - (share your experience, but constructively)
+
+
+
+
+

Keypoints

+
    +

  • Without reproducibility in scientific computing, everyone would have to start a new project / code from scratch

    • +
+
+
+
+
+

Organizing your projects

+
+

Objectives

+
    +

  • Get an overview on how to organize research projects

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching incl. discussions

    • +
+
+

One of the first steps to make your work reproducible is to organize your projects well. +Let’s go over some of the basic things which people have found to work (and not to work).

+
+

Directory structure for projects

+
    +

  • Project files in a single folder

    • +

  • Different projects should have separate folders

    • +

  • Use consistent and informative directory structure

    +
      +

    • Avoid spaces in directory and file names – it is uglier for humans but handy for computers.

      • +
    +
    • +

  • If you need to separate public/private, you can put them in public and private Git repos

    +
      +

    • If you need to separate public/secret, use .gitignore or a separate folder that’s not in Git

      • +
    +
    • +

  • Add a README file to describe the project and instructions on reproducing the results

    • +

  • If a software is reused in several projects it can make sense to put them in own repo

    • +
+

A project directory can look something like this:

+
project_name/
+├── README.md             # overview of the project
+├── data/                 # data files used in the project
+│   ├── README.md         # describes where data came from
+│   └── sub-folder/       # may contain subdirectories
+├── processed_data/       # intermediate files from the analysis
+├── manuscript/           # manuscript describing the results
+├── results/              # results of the analysis (data, tables, figures)
+├── src/                  # contains all code in the project
+│   ├── LICENSE           # license for your code
+│   ├── requirements.txt  # software requirements and dependencies
+│   └── ...
+└── doc/                  # documentation for your project
+    ├── index.rst
+    └── ...
+
+
+
+
+
+

Tracking source code, data, and results

+
    +

  • All code is version controlled and goes in the src/ or source/ directory

    • +

  • Include appropriate LICENSE file and information on software requirements

    • +

  • You can also version control data files or input files under data/

    • +

  • If data files are too large (or sensitive) to track, untrack them using .gitignore

    • +

  • Intermediate files from the analysis are kept in processed_data/

    • +

  • Consider using Git tags to mark specific versions of results (version +submitted to a journal, dissertation version, poster version, etc.):

    +
    $ git tag -a thesis-submitted -m "this is the submitted version of my thesis"
+
    +
    +
    • +
+ +
+
+
+

Discussion on reproducibility

+
+

Discuss in the collaborative document:

+

How do you collaborate on writing academic papers?

+
- Are you using version control for academic papers?
+  - ...
+  - ...
+  - (share your experience)
+
+- How do you handle collaborative issues e.g. conflicting changes?
+  - ...
+  - ...
+  - (share your experience)
+
+
+
+

Please write or discuss your ideas before opening solution!

+
+ +
+
+
+

Some tools and templates

+ +

More tools and templates in Heidi Seibolds blog.

+
+
+

Reproducible publications

+
    +

  • Git can be used to collaborate on manuscripts written in, e.g., LaTeX and other text-based formats but other tools exist, some with git integration:

    +
      +

    • Overleaf or Typst: online, collaborative LaTeX editor

      • +

    • Authorea: collaborative platform for preprints

      • +

    • HackMD or HedgeDoc: online collaborative Markdown editors

      • +

    • Manuscripts.io: a collaborative authoring tool that support scientific content and reproducibility.

      • +

    • Google Docs can be a good alternative

      • +
    +
    • +

  • Many tools exist to assist in making scholarly output reproducible:

    +
      +

    • rrtools: instructions, templates, and functions for writing a reproducible article or report with R.

      • +

    • Jupyter Notebooks: web-based computational environment for creating code and text based notebooks that can be used as, see also our Jupyter lesson later in this workshop. +supplementary material for articles.

      • +

    • Binder: makes a repository with Jupyter notebooks available in an executable environment (discussed later in the Jupyter lesson).

      • +

    • “Research compendia”: a set of good practices for +reproducible data analysis in R, but much is transferable to other languages.

      • +
    +
    • +
+
+

See also

+

Do you want to practice your reproducibility skills and get inspired by working with other people’s code/data? Join a ReproHack event!

+
+
+

Keypoints

+
    +

  • An organized project directory structure helps with reproducibility.

    • +
+
+
+
+
+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+
+

Recording dependencies

+
+

Questions

+
    +

  • How can we communicate different versions of software dependencies?

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching

    • +

  • 10 min demo

    • +
+
+

Our codes often depend on other codes that in turn depend on other codes …

+
    +

  • Reproducibility: We can version-control our code with Git but how should we version-control dependencies? +How can we capture and communicate dependencies?

    • +

  • Dependency hell: Different codes on the same environment can have conflicting dependencies.

    • +
+
+An image showing blocks (=codes) depending on each other for stability +
+

From xkcd - dependency. Another image that might be familiar to some of you working with Python can be found on xkcd - superfund.

+
+
+
+

Kitchen analogy

+
    +

  • Software <-> recipe

    • +

  • Data <-> ingredients

    • +

  • Libraries <-> cooking books/blogs

    • +
+
+Cooking recipe in an unfamiliar language +
+

Cooking recipe in an unfamiliar language [Midjourney, CC-BY-NC 4.0]

+
+
+
+Kitchen with few open cooking books +
+

When we create recipes, we often use existing recipes written by others (libraries) [Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+

Tools and what problems they try to solve

+

Conda, Anaconda, pip, virtualenv, Pipenv, pyenv, Poetry, requirements.txt, +environment.yml, renv, …, these tools try to solve the following problems:

+
    +

  • Defining a specific set of dependencies, possibly with well defined versions

    • +

  • Installing those dependencies mostly automatically

    • +

  • Recording the versions for all dependencies

    • +

  • Isolate environments

    +
      +

    • On your computer for projects so they can use different software

      • +

    • Isolate environments on computers with many users (and allow self-installations)

      • +
    +
    • +

  • Using different Python/R versions per project

    • +

  • Provide tools and services to share packages

    • +
+

Isolated environments are also useful because they help you make sure +that you know your dependencies!

+

If things go wrong, you can delete and re-create - much better +than debugging. The more often you re-create your environment, the +more reproducible it is.

+
+
+
+

Demo

+
+

Dependencies-1: Time-capsule of dependencies

+

Situation: 5 students (A, B, C, D, E) wrote a code that depends on a couple of libraries. +They uploaded their projects to GitHub. We now travel 3 years into the future +and find their GitHub repositories and try to re-run their code before adapting +it.

+

Answer in the collaborative document:

+
    +

  • Which version do you expect to be easiest to re-run? Why?

    • +

  • What problems do you anticipate in each solution?

    +
    +

    A: +You find a couple of library imports across the code but that’s it.

    +

    B: +The README file lists which libraries were used but does not mention +any versions.

    +

    C: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy
+  - numpy
+  - sympy
+  - click
+  - python
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@master
+    - git+https://github.com/anotheruser/anotherproject.git@master
+
    +
    +

    D: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - pip
+  - pip:
+    - git+https://github.com/someuser/someproject.git@d7b2c7e
+    - git+https://github.com/anotheruser/anotherproject.git@sometag
+
    +
    +

    E: +You find a environment.yml file with:

    +
    name: student-project
+channels:
+  - conda-forge
+dependencies:
+  - scipy=1.3.1
+  - numpy=1.16.4
+  - sympy=1.4
+  - click=7.0
+  - python=3.8
+  - someproject=1.2.3
+  - anotherproject=2.3.4
+
    +
    +
    + +
    • +
+
+
+

Dependencies-2: Create a time-capsule for the future

+

Now we will demo creating our own time-capsule and share it with the future +world. If we asked you now which dependencies your project is using, what would +you answer? How would you find out? And how would you communicate this +information?

+
+

Try this either with your own project or inside the “coderefinery” conda +environment:

+
$ conda env export > environment.yml
+
+
+

Have a look at the generated file and discuss what you see.

+

In future you can re-create this environment with:

+
$ conda env create -f environment.yml
+
+
+

More information: https://docs.conda.io/en/latest/

+

See also: https://github.com/mamba-org/mamba

+
+
+
+

Keypoints

+
    +

  • Recording dependencies with versions can make it easier for the next person to execute your code

    • +

  • There are many tools to record dependencies

    • +
+
+
+
+
+

Recording environments

+
+

Objectives

+
    +

  • Understand what containers are

    • +

  • Understand good and less good usecases for containers

    • +

  • Discuss container definitions files in the context of reusability and +reproducibility

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +

  • 10 min demo

    • +
+
+
+

What is a container?

+

Imagine if you didn’t have to install things yourself, but instead you could +get a computer with the exact software for a task pre-installed? Containers +effectively do that, with various advantages and disadvantages. They are +like an entire operating system with software installed, all in one file.

+
+He said, then we will ship your machine. And that's how Docker was born. +
+

From reddit.

+
+
+
+

Kitchen analogy

+
    +

  • Our codes/scripts <-> cooking recipes

    • +

  • Container definition files <-> like a blueprint to build a kitchen with all +utensils in which the recipe can be prepared.

    • +

  • Container images <-> example kitchens

    • +

  • Containers <-> identical factory-built mobile food truck kitchens

    • +
+

Just for fun: which operating systems do the following example kitchens represent?

+
+
+Generated image of a kitchen +
+

[Midjourney, CC-BY-NC 4.0]

+
+
+
+
+
+
+

From definition files to container images to containers

+
    +

  • Containers can be built to bundle all the necessary ingredients (data, code, environment, operating system).

    • +

  • A container image is like a piece of paper with all the operating system on it. When you run it, +a transparent sheet is placed on top to form a container. The container runs and writes only on +that transparent sheet (and what other mounts have been layered on top). When you are done, +transparency is thrown away. It can be repeated as often as you want, and base is always the same.

    • +

  • Definition files (e.g. Dockerfile or Singularity definition file) are text +files that contain a series of instructions to build container images.

    • +
+
+
+

You may have use for containers in different ways

+
    +

  • Installing a certain software is tricky, or not supported for your operating system? -> See if an image is available and run the software from a container instead!

    • +

  • You want to make sure your colleagues are using the same environment for running your code? -> Provide them an image of your container!

    +
      +

    • If this does not work, because they are using a different architecture than you do? -> Provide a definition file for them to build the image suitable to their computers. This does not create the exact environment as you have, but in most cases similar enough.

      • +
    +
    • +
+
+
+

The container recipe

+

Here is an example of a Singularity definition file (reference):

+
Bootstrap: docker
+From: ubuntu:20.04
+
+%post
+    apt-get -y update
+    apt-get -y install cowsay lolcat
+
+%environment
+    export LC_ALL=C
+    export PATH=/usr/games:$PATH
+
+%runscript
+    date | cowsay | lolcat
+
+
+

Popular container implementations:

+ +

They are to some extent interoperable:

+
    +

  • podman is very close to Docker

    • +

  • Docker images can be converted to Singularity/Apptainer images

    • +

  • Singularity Python can convert Dockerfiles to Singularity definition files

    • +
+
+
+
+

Pros and cons of containers

+

Containers are popular for a reason - they solve a number of +important problems:

+
    +

  • Allow for seamlessly moving workflows across different platforms.

    • +

  • Can solve the “works on my machine” situation.

    • +

  • For software with many dependencies, in turn with its own dependencies, +containers offer possibly the only way to preserve the +computational experiment for future reproducibility.

    • +

  • A mechanism to “send the computer to the data” when data is too

    • +

  • Installing software into a file instead of into your computer (removing +a file is often easier than uninstalling software if you suddenly regret an +installation)

    • +
+

However, containers may also have some drawbacks:

+
    +

  • Can be used to hide away software installation problems and thereby +discourage good software development practices.

    • +

  • Instead of “works on my machine” problem: “works only in this container” problem?

    • +

  • They can be difficult to modify (this is the focus of an exercise below)

    • +

  • Container images can become large

    • +
+
+

Danger

+

Use only official and trusted images! Not all images can be trusted! There +have been examples of contaminated images so investigate before using images +blindly. Apply same caution as installing software packages from untrusted +package repositories.

+
+
+
+
+

Where can one share or find images?

+ +
+
+
+

Exercises

+
+

Containers-1: Time travel

+

Scenario: A researcher has written and published their research code which +requires a number of libraries and system dependencies. They ran their code +on a Linux computer (Ubuntu). One very nice thing they did was to publish +also a container image with all dependencies included, as well as the +definition file (below) to create the container image.

+

Now we travel 3 years into the future and want to reuse their work and adapt +it for our data. The container registry where they uploaded the container +image however no longer exists. But luckily we still have the definition file +(below)! From this we should be able to create a new container image.

+
    +

  • Can you anticipate problems using the definitions file 3 years after its creation? +Which possible problems can you point out?

    • +

  • Discuss possible take-aways for creating more reusable containers.

    • +
+
+
 1Bootstrap: docker
+ 2From: ubuntu:latest
+ 3
+ 4%post
+ 5    # Set environment variables
+ 6    export VIRTUAL_ENV=/app/venv
+ 7
+ 8    # Install system dependencies and Python 3
+ 9    apt-get update && \
+10    apt-get install -y --no-install-recommends \
+11        gcc \
+12        libgomp1 \
+13        python3 \
+14        python3-venv \
+15        python3-distutils \
+16        python3-pip && \
+17    apt-get clean && \
+18    rm -rf /var/lib/apt/lists/*
+19
+20    # Set up the virtual environment
+21    python3 -m venv $VIRTUAL_ENV
+22    . $VIRTUAL_ENV/bin/activate
+23
+24    # Install Python libraries
+25    pip install --no-cache-dir --upgrade pip && \
+26    pip install --no-cache-dir -r /app/requirements.txt
+27
+28%files
+29    # Copy project files
+30    ./requirements.txt /app/requirements.txt
+31    ./app.py /app/app.py
+32    # Copy data
+33    /home/myself/data /app/data
+34    # Workaround to fix dependency on fancylib
+35    /home/myself/fancylib /usr/lib/fancylib
+36
+37%environment
+38    # Set the environment variables
+39    export LANG=C.UTF-8 LC_ALL=C.UTF-8
+40    export VIRTUAL_ENV=/app/venv
+41
+42%runscript
+43    # Activate the virtual environment
+44    . $VIRTUAL_ENV/bin/activate
+45    # Run the application
+46    python /app/app.py
+
+
+ +
+
+
+

(optional) Containers-2: Explore two really useful Docker images

+

You can try the below if you have Docker installed. If you have +Singularity/Apptainer and not Docker, the goal of the exercise can be to run +the Docker containers through Singularity/Apptainer.

+
    +

  1. Run a specific version of Rstudio:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio
+
    +
    +

    Then open your browser to http://localhost:8787 +with login rstudio and password “yourpasswordhere” used in the previous +command.

    +

    If you want to try an older version you can check the tags at +https://hub.docker.com/r/rocker/rstudio/tags +and run for example:

    +
    $ docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio:3.3
+
    +
    +
    2. +

  2. Run a specific version of Anaconda3 from +https://hub.docker.com/r/continuumio/anaconda3:

    +
    $ docker run -i -t continuumio/anaconda3 /bin/bash
+
    +
    +
    3. +
+
+
+
+

Resources for further learning

+ +
+

Keypoints

+
    +

  • Containers can be helpful if complex setups are needed to running a specific software

    • +

  • They can also be helpful for prototyping without “messing up” your own computing environment, or for running software that requires a different operating system than your own

    • +
+
+
+
+
+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
+
+
+
+
+
+

List of exercises

+
+

Full list

+

This is a list of all exercises and solutions in this lesson, mainly +as a reference for helpers and instructors. This list is +automatically generated from all of the other pages in the lesson. +Any single teaching event will probably cover only a subset of these, +depending on their interests.

+
+
+
+

Instructor guide

+
+

Detailed day schedule

+

Two example schedules for this lesson:

+

This is the planned schedule for the workshop in September 2023 (2 hours and 5 minutes including 10 min break) ; note that for this workshop, sharing code and data was moved to social coding lesson:

+ +

This was the schedule at workshop in March 2023 (2 hours and 15 minutes including 2x 10 min break):

+ +
+
+

Why we teach this lesson

+

Reproducibility in research is something that publishers, funding agencies, universities, +research leaders and the general public worries about and much is being written about it. +It is also something that researchers care deeply about - this lesson is typically one of the +most popular lessons in the pre-workshop survey.

+

Even though most PhD students, postdocs and researchers (i.e. typical workshop participants) +know about the importance of reproducibility in research, they often lack both a general +overview of what different aspects there are to reproducibility, and the knowledge of +specific tools that can be used for improving reproducibility.

+

Many participants may not adhere to good practices when organizing their projects, +and the “Organizing your projects” episode is meant to encourage participants to +structure their projects better. This may be obvious to some participants but it +doesn’t harm to preach to the choir.

+

Even though many participants know that code can have many dependencies (e.g. they +may have experienced difficulties in getting other people’s code to run), they +often don’t know or use good practices when it comes to recording dependencies. +Most participants also don’t use isolated environments for different projects and +don’t know why that can be important. +The episode “Recording dependencies” tries to convey the importance of recording +dependencies accurately for your projects, and shows how tools like conda can be +used both as a package and software environment manager.

+

Many participants have heard about containers and find them interesting, but +lack an understanding of how they work or how they can be used. The episode +“Recording environments” introduces the concept of containers, and the optional +episode “Creating and sharing a container image” goes into details.

+

Many participants use complicated series of computational steps in their research +without realizing that this work falls into the category of “scientific workflows”, +and that there actually exist tools that help make such workflows reproducible. +The episode “Recording computational steps” introduces the concept of scientific +workflows, discusses various ways of managing workflows with varying degrees of +reproducibility, and shows how tools like Snakemake can be used to +both simplify workflows and make them more reproducible.

+
+
+

How to teach this lesson

+
+

How to start

+

Everyone knows that scientific results need to be reproducible, but not everyone is using +appropriate tools to ensure this. Here we’re going to get to know tools which help with +preserving the provenance of data and reproducibility on different levels, ranging from +workflow automation to software environment (containers).

+
+
+

Focus on concepts, and when to use which tool

+

Try to explain better what the different tools are useful for, but don’t go +into details. In this lesson we are not trying to gain expertise in the +various tools and master the details but rather we want to give an overview and +show that many tools exist and try to give participant the right feel for which +set of tools to approach for which type of problem.

+
+
+
+

Typical pitfalls

+
+

Indentation in Snakefiles

+
    +

  • the body of a rule and the body of an input keyword need to be indented, but the number of spaces doesn’t matter +This works:

    • +
+
rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+
+

but this doesn’t work:

+
rule all:
+    input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+

nor this:

+
rule all:
+input:
+    expand('statistics/{book}.data', book=DATA),
+    expand('plot/{book}.png', book=DATA)
+
+
+
+
+
+

Field reports

+
+

2022 September

+

We used the strategy “absolutely minimal introductions, most time +for exercise”. Overall, it was probably the right thing to do since +there is so little time and so much to cover.

+

There wasn’t enough time for the conda exercise (we could give only 7 +minutes), but also I wonder how engaging it is. We should look at how +to optimize the start of that episode.

+

The Snakemake episode went reasonably well. Our goal was 5 minutes +intro, long exercise, 5 minutes outro. The intro was actually a bit +longer, and there was the comment that we didn’t really explain what +Snakemake was before it started (though we tried). The start of this +episode should get particular focus in the future, since this is the +main exercise of the day.

+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/singlehtml/objects.inv b/singlehtml/objects.inv new file mode 100644 index 0000000..e7c16bd Binary files /dev/null and b/singlehtml/objects.inv differ diff --git a/where-to-go/index.html b/where-to-go/index.html new file mode 100644 index 0000000..bdc8a2d --- /dev/null +++ b/where-to-go/index.html @@ -0,0 +1,228 @@ + + + + + + + Where to go from here — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Where to go from here

+
+

Objectives

+
    +

  • Understand when tools discussed in this episode can be useful

    • +
+
+
+

Instructor note

+
    +

  • 10 min teaching/discussion

    • +
+
+

This episode presents a lot of different tools and opportunities for your research software project. +However, you will not always need all of them. As with so many things, it again depends on your project.

+
+

Important for every project

+
    +

  • Clear file structure for your project

    • +

  • At least consider the possibility that someone, maybe you may want to reproduce your work

    +
      +

    • Can you do something (small) to make it easier?

      • +

    • If you have ideas, but no time: add an issue to your repository; maybe someone else wants to help.

      • +
    +
    • +
+
+
+

Workflow tools will maybe make sense in the future

+
    +

  • In many cases, it is probably not needed

    • +

  • You will want to consider workflow tools:

    +
      +

    • When processing many files with many steps

      • +

    • Steps or files may change

      • +

    • Your main script, connecting your steps gets very long

      • +

    • …

      • +
    +
    • +
+
+
+

When should I worry about dependencies?

+
    +

  • Your code depends on multiple other packages

    • +

  • You want to avoid questions like: “What do I need to install to run your code”

    • +

  • You want help yourself running your code

    +
      +

    • After a few years

      • +

    • On a different computer

      • +

    • …

      • +
    +
    • +
+
+
+

Containers seem amazing, but do I have use for them?

+
    +

  • Maybe not yet, but knowing that you can …

    +
      +

    • Run Linux tools on your Windows computer

      • +

    • Run different versions of same software on your computer

      • +

    • Follow the “easy installation instructions” for an operating system that is not your own

      • +

    • Get a fully configured environment instead of only installing a tool

      • +

    • Share your setup and configurations with others +… can be very beneficial :)

      • +
    +
    • +
+
+

Keypoints

+
    +

  • Not everything in this lesson might be useful right now, but it is good to know that these things exist if you ever get in a situation that would require such solution.

    • +

  • Caring about reproducibility makes work easier for the next person working on the project - and that might be you in a few years!

    • +
+
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+
+ + +
+
+ +
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+
+ + + + \ No newline at end of file diff --git a/workflow-management/index.html b/workflow-management/index.html new file mode 100644 index 0000000..1c9f0d7 --- /dev/null +++ b/workflow-management/index.html @@ -0,0 +1,394 @@ + + + + + + + Recording computational steps — Reproducible research documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Recording computational steps

+
+

Questions

+
    +

  • You have some steps that need to be run to do your work. How do you +actually run them? Does it rely on your own memory and work, or is it +reproducible? How do you communicate the steps for future you and others?

    • +

  • How can we create a reproducible workflow?

    • +

  • When to use scientific workflow management systems.

    • +
+
+
+

Instructor note

+
    +

  • 5 min teaching

    • +

  • 15 min demo

    • +
+
+
+

Several steps from input data to result

+

The following material is partly derived from a HPC Carpentry lesson.

+

In this episode, we will use an example +project which finds most frequent +words in books and plots the result from those statistics. In this example we +wish to:

+
    +

  1. Analyze word frequencies using statistics/count.py +for 4 books +(they are all in the data directory).

    2. +

  2. Plot a histogram using plot/plot.py.

    3. +
+
+From book to word counts to plot +
+

Example (for one book only):

+
$ python statistics/count.py data/isles.txt > statistics/isles.data
+$ python plot/plot.py --data-file statistics/isles.data --plot-file plot/isles.png
+
+
+

Another way to analyze the data would be via a graphical user interface (GUI), where you can for example drag and drop files and click buttons to do the different processing steps.

+

Both of the above (single line commands and simple graphical interfaces) are tricky in terms of reproducibility. We currently have two steps and 4 books. But imagine having 4 steps and 500 books. +How could we deal with this?

+

As a first idea we could express the workflow with a script. The repository includes such script called run_all.sh.

+

We can run it with:

+
$ bash run_all.sh
+
+
+

This is imperative style: we tell the script to run these +steps in precisely this order, as we would run them manually, one after another.

+
+

Discussion

+
    +

  • What are the advantages of this solution compared to processing all one by one?

    • +

  • Is the scripted solution reproducible?

    • +

  • Imagine adding more steps to the analysis and imagine the steps being time consuming. What problems do you anticipate +with a scripted solution?

    + +
    • +
+
+
+
+
+

Workflow tools

+

Sometimes it may be helpful to go from imperative to declarative style. Rather than saying “do this and then that” we describe dependencies but we let the tool figure out the series of steps to produce results.

+
+

Example workflow tool: Snakemake

+

Snakemake (inspired by GNU Make) is one of many tools to create reproducible and scalable data analysis workflows. Workflows are described via a human readable, Python based language. +Snakemake workflows scale seamlessly from laptop to cluster or cloud, without the need to modify the workflow definition.

+
+
+
+
+

A demo

+
+

Preparation

+

The exercise (below) and pre-exercise discussion uses the +word-count repository +(https://github.com/coderefinery/word-count) which we need to clone to work on it.

+

If you want to do this exercise on your own, you can do so either on your own computer (follow the instructions in the bottom right panel on the CodeRefinery installation instruction page), or the Binder +cloud service:

+

On your own computer:

+
    +

  • Install the necessary tools

    • +

  • Activate the coderefinery conda environment with conda activate coderefinery.

    • +

  • Clone the word-count repository:

    +
    $ git clone https://github.com/coderefinery/word-count.git
+
    +
    +
    • +
+

On Binder: +We can also use the cloud service Binder to make sure +we all have the same computing environment. This is interesting from a +reproducible research point of view and it’s explained further in the Jupyter +lesson how this is even +possible.

+
    +

  • Go to https://github.com/coderefinery/word-count and click on the “launch binder” badge in the README.

    • +

  • Once it get started, you can open a new Terminal from the new menu (top right) and select Terminal.

    • +
+
+
+

Workflow-1: Workflow solution using Snakemake

+
+How Snakemake works +
+

Somebody wrote a Snakemake solution in the Snakefile:

+
# a list of all the books we are analyzing
+DATA = glob_wildcards('data/{book}.txt').book
+
+rule all:
+    input:
+        expand('statistics/{book}.data', book=DATA),
+        expand('plot/{book}.png', book=DATA)
+
+# count words in one of our books
+rule count_words:
+    input:
+        script='code/count.py',
+        book='data/{file}.txt'
+    output: 'statistics/{file}.data'
+    shell: 'python {input.script} {input.book} > {output}'
+
+# create a plot for each book
+rule make_plot:
+    input:
+        script='code/plot.py',
+        book='statistics/{file}.data'
+    output: 'plot/{file}.png'
+    shell: 'python {input.script} --data-file {input.book} --plot-file {output}'
+
+
+
+

We can see that Snakemake uses declarative style: +Snakefiles contain rules that relate targets (output) to dependencies +(input) and commands (shell).

+

Steps:

+
    +

  1. Clone the example to your computer: $ git clone https://github.com/coderefinery/word-count.git

    2. +

  2. Study the Snakefile. How does it know what to do first and what to do then?

    3. +

  3. Try to run it. Since version 5.11 one needs to specify number of cores (or +jobs) using -j, --jobs or --cores:

    +
    $ snakemake --delete-all-output -j 1
+$ snakemake -j 1
+
    +
    +

    The --delete-all-output part makes sure that we remove all generated files before we start.

    +
    4. +

  4. Try running snakemake again and observe that and discuss why it refused to rerun all steps:

    +
    $ snakemake -j 1
+
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
+
    +
    +
    5. +

  5. Make a tiny modification to the plot.py script and run $ snakemake -j 1 again and observe how it will only re-run the plot steps.

    6. +

  6. Make a tiny modification to one of the books and run $ snakemake -j 1 again and observe how it only regenerates files for this book.

    7. +

  7. Discuss possible advantages compared to a scripted solution.

    8. +

  8. Question for R developers: Imagine you want to rewrite the two Python scripts and use R instead. Which lines in +the Snakefile would you have to modify so that it uses your R code?

    9. +

  9. If you make changes to the Snakefile, validate it using $ snakemake --lint.

    10. +
+ +
+
+
+

Visualizing the workflow

+

We can visualize the directed acyclic graph (DAG) of our current Snakefile +using the --dag option, which will output the DAG in dot language.

+

Note: This requires the Graphviz software, +which can be installed by conda install graphviz.

+
$ snakemake -j 1 --dag | dot -Tpng > dag.png
+
+
+

Rules that have yet to be completed are indicated with solid outlines, while already completed rules are indicated with dashed outlines.

+
+Snakemake DAG +
+
+
+

Why Snakemake?

+
    +

  • Gentle learning curve.

    • +

  • Free, open-source, and installs easily via conda or pip.

    • +

  • Cross-platform (Windows, MacOS, Linux) and compatible with all High Performance Computing (HPC) schedulers: +same workflow works without modification and scales appropriately whether on a laptop or cluster.

    • +

  • If several workflow steps are independent of each other, and you have multiple cores available, Snakemake can run them in parallel.

    • +

  • Is is possible to define isolated software environments per rule, e.g. by adding conda: 'environment.yml' to a rule.

    • +

  • Also possible to run workflows in Docker or Apptainer containers e.g. by adding container: 'docker://some-org/some-tool#2.3.1' to a rule.

    • +

  • Heavily used in bioinformatics, but is completely general.

    • +

  • Nice functionality for archiving the workflow, see: the official documentation

    • +
+

Tools like Snakemake help us with reproducibility by supporting us with automation, scalability and portability of our workflows.

+
+
+

Similar tools

+ +
+

Keypoints

+
    +

  • Computational steps can be recorded in many ways

    • +

  • Workflow tools can help, if there are many steps to be executed

    • +
+
+
+
+ + +
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+
+ + + + \ No newline at end of file