From f597b4c59382d9afc92cead04e53626144a7d030 Mon Sep 17 00:00:00 2001 From: mwakok Date: Wed, 24 Jul 2024 11:21:27 +0000 Subject: [PATCH] deploy: 6bdbd772b837b212b446e1d81cffc02094a46942 --- _sources/software/project_cards.md | 105 ++++++++++++---------------- searchindex.js | 2 +- software/project_cards.html | 107 ++++++++++++----------------- 3 files changed, 90 insertions(+), 124 deletions(-) diff --git a/_sources/software/project_cards.md b/_sources/software/project_cards.md index 0c20374..0d79265 100644 --- a/_sources/software/project_cards.md +++ b/_sources/software/project_cards.md @@ -10,31 +10,28 @@ Add the cards below as issues to your repository to track the progress of adopti ^^^ ```md -_Essential_ +_Essential_ - [ ] Use [git](https://www.atlassian.com/git) as a version control system - [ ] Upload your project on [GitHub](https://github.com/) or [TU Delft GitLab](https://gitlab.tudelft.nl/) _Recommended_ - [ ] Make your repository [public](https://coderefinery.github.io/social-coding/) -- [ ] [Branch hygiene](https://coderefinery.github.io/git-branch-design/) -- [ ] [Meaningful commit messages](https://www.git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project#_commit_guidelines) +- [ ] Consider your [branch hygiene](https://coderefinery.github.io/git-branch-design/) +- [ ] Use a branching model (e.g. [GitFlow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow)) +- [ ] Use [meaningful commit messages](https://www.git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project#_commit_guidelines) ``` --- -**Dependency management** +**Collaboration** ^^^ ```md -_Essential_ -- [ ] Document your project dependencies -- [ ] Provide instructions for replicating the computational environment +_Essential_ +- [ ] Make use of [GitHub issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) _Recommended_ -- [ ] Use a [dependency manager](https://the-turing-way.netlify.app/reproducible-research/renv/renv-package.html) -- [ ] Pin [exact versions](https://github.com/conda/conda-lock) used to generate your environment - -_Optional_ -- [ ] [Containerized workflow](https://the-turing-way.netlify.app/reproducible-research/renv/renv-containers.html) +- [ ] [Contribution guidelines](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors) +- [ ] [Code of conduct](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-code-of-conduct-to-your-project) ``` --- @@ -43,13 +40,9 @@ _Optional_ ```md _Essential_ -- [ ] [README](https://github.com/18F/open-source-guide/blob/18f-pages/pages/making-readmes-readable.md) -- [ ] [LICENSE](https://doi.org/10.5281/zenodo.4629662) +- [ ] [README](https://www.makeareadme.com) +- [ ] Apply a TU Delft pre-approved [LICENSE](https://zenodo.org/records/4629635) - [ ] [CITATION](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) - -_Recommended_ -- [ ] Make use of [Github issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) -- [ ] [Code of conduct](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-code-of-conduct-to-your-project) ``` --- @@ -58,34 +51,19 @@ _Recommended_ ```md _Essential_ +- [ ] Source code documentation ([docstrings](https://numpydoc.readthedocs.io/en/latest/format.html)) +- [ ] Document your project dependencies - [ ] Installation instructions - [ ] User documentation -- [ ] Developer documentation -- [ ] Source code documentation ([docstrings](https://numpydoc.readthedocs.io/en/latest/format.html)) _Recommended_ -- [ ] Examples and tutorials (Jupyter notebooks, videos, screencasts) -- [ ] Automate documentation building with [sphinx](https://coderefinery.github.io/sphinx-lesson/) -- [ ] Website ([github.io pages](https://pages.github.com/), [Readthedocs](https://readthedocs.org/), [JupyterBook](https://jupyterbook.org/intro.html)) - -_Optional_ -- [ ] Build [API reference](https://developer.lsst.io/python/numpydoc.html) from docstrings -``` +- [ ] Developer documentation and setup +- [ ] Examples and tutorials (e.g. Jupyter Notebooks) ---- -**Collaboration** -^^^ - -```md -_Essential_ -- [ ] Make use of [Github issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) -- [ ] Provide contribution [guidelines](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors) - -_Recommended_ -- [ ] Choose a branching model ([DCC Guides on branches](https://tu-delft-dcc.github.io/software/git/branch_management.html)) -- [ ] Make use of [issue templates](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository) -- [ ] Provide a [Code of Conduct](https://www.contributor-covenant.org/) -- [ ] Use [semantic versioning](https://semver.org/) for your releases +_Optional_ +- [ ] Documentation tools ([Sphinx](https://coderefinery.github.io/documentation/sphinx/), [JupyterBook](https://jupyterbook.org/intro.html), [Quarto](https://quarto.org/docs/guide/)) +- [ ] Build an [API reference](https://developer.lsst.io/python/numpydoc.html) from docstrings +- [ ] Hosting ([GitHub Pages](https://pages.github.com/), [Readthedocs](https://readthedocs.org/)) ``` --- @@ -94,30 +72,35 @@ _Recommended_ ```md _Essential_ -- [ ] Document verification of user installation -- [ ] Document how users can verify the proper functioning of the software +- [ ] Installation/execution verification -_Recommended_ -- [ ] [Defensive programming](https://swcarpentry.github.io/python-novice-inflammation/10-defensive/index.html) +_Recommended_ +- [ ] [Defensive programming](https://swcarpentry.github.io/python-novice-inflammation/10-defensive.html) - [ ] Test your software with [integration tests](https://the-turing-way.netlify.app/reproducible-research/testing/testing-integrationtest.html) and [unit tests](https://the-turing-way.netlify.app/reproducible-research/testing/testing-unittest.html) -- [ ] Make use of [Continuous Integration](https://the-turing-way.netlify.app/reproducible-research/ci/ci-options.html) -- [ ] Code coverage check ([Codecov](https://about.codecov.io/), [Sonarcloud](https://sonarcloud.io/), [Travis](https://www.travis-ci.com/)) +- [ ] Make use of [Continuous Integration](https://coderefinery.github.io/testing/continuous-integration/) to automate testing + +_Optional_ +- [ ] Code coverage check (e.g. [Sonarcloud](https://sonarcloud.io/), [codecov](https://about.codecov.io)) ``` --- -**Code quality** +**Software quality** ^^^ -```md +```md _Essential_ -- [ ] Project [organisation](https://coderefinery.github.io/reproducible-research/organizing-projects/) -- [ ] Record [software dependencies](https://coderefinery.github.io/reproducible-research/dependencies/) +- [ ] [Organize](https://coderefinery.github.io/reproducible-research/organizing-projects/) your project for reproducibility +- [ ] [Record and manage](https://coderefinery.github.io/reproducible-research/dependencies/) your software dependencies _Recommended_ -- [ ] Follow a consistent code style, such as [PEP8 guidelines](https://realpython.com/python-pep8/) -- [ ] Use a linter ([pylint](https://pypi.org/project/pylint/), [flake8](https://pypi.org/project/flake8/)) -- [ ] Use a formatter ([black](https://github.com/psf/black), [yapf](https://github.com/google/yapf)) +- [ ] Make [refactoring](https://refactoring.guru/refactoring) part of your workflow - [ ] Follow [best coding practices](https://alan-turing-institute.github.io/rse-course/html/module07_construction_and_design/index.html) + +_Recommended for Python_ +- [ ] Follow [PEP8 guidelines](https://realpython.com/python-pep8/) +- [ ] Use a tool for dependency management (e.g. [poetry](https://the-turing-way.netlify.app/reproducible-research/renv/renv-package.html)) +- [ ] Use linter (e.g. [pylint](https://pypi.org/project/pylint/), [flake8](https://pypi.org/project/flake8/)) +- [ ] Use a formatter (e.g. [black](https://github.com/psf/black)) ``` --- @@ -126,15 +109,17 @@ _Recommended_ ```md _Essential_ -- [ ] Obtain a DOI from ([Zenodo](https://zenodo.org/) or [4TU.ResearchData](https://data.4tu.nl/info/about-your-data/getting-started)) +- [ ] Obtain a DOI ([Zenodo](https://zenodo.org/) or [4TU.ResearchData](https://data.4tu.nl/info/about-your-data/getting-started)) _Recommended_ -- [ ] [Semantic versioning](https://semver.org/) -- [ ] Tagged releases ([GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github)) +- [ ] Use [semantic versioning](https://semver.org/) +- [ ] Create tagged releases ([GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github)) - [ ] [CHANGELOG](https://keepachangelog.com/en/1.0.0/) -- [ ] Upload to registry ([PyPI](https://realpython.com/pypi-publish-python-package/), [conda](https://conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html), [DockerHub](https://docs.docker.com/docker-hub/repos/)) -- [ ] [Release guide](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository) -- [ ] [Continuous Integration](https://the-turing-way.netlify.app/reproducible-research/ci/ci-options) for build and release +- [ ] Upload to [registry](https://github.com/NLeSC/awesome-research-software-registries) (e.g. [PyPI](https://realpython.com/pypi-publish-python-package/), [conda](https://conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html)) +- [ ] [Releasing guide](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository) + +_Optional_ +- [ ] [Continuous Integration](https://the-turing-way.netlify.app/reproducible-research/ci/ci-options.html) for automated build and release ``` ```` diff --git a/searchindex.js b/searchindex.js index e313db5..95c9330 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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\ No newline at end of file diff --git a/software/project_cards.html b/software/project_cards.html index bd857bb..e8c168d 100644 --- a/software/project_cards.html +++ b/software/project_cards.html @@ -425,14 +425,15 @@

FAIR assessment cardsVersion Control

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_Essential_  
+
_Essential_
 - [ ] Use [git](https://www.atlassian.com/git) as a version control system 
 - [ ] Upload your project on [GitHub](https://github.com/) or [TU Delft GitLab](https://gitlab.tudelft.nl/)
 
 _Recommended_  
 - [ ] Make your repository [public](https://coderefinery.github.io/social-coding/)
-- [ ] [Branch hygiene](https://coderefinery.github.io/git-branch-design/)
-- [ ] [Meaningful commit messages](https://www.git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project#_commit_guidelines)
+- [ ] Consider your [branch hygiene](https://coderefinery.github.io/git-branch-design/)
+- [ ] Use a branching model (e.g. [GitFlow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow))
+- [ ] Use [meaningful commit messages](https://www.git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project#_commit_guidelines)
@@ -441,19 +442,15 @@

FAIR assessment cards
-

Dependency management

+

Collaboration

-
_Essential_
-- [ ] Document your project dependencies
-- [ ] Provide instructions for replicating the computational environment
+
_Essential_  
+- [ ] Make use of [GitHub issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues)
 
 _Recommended_
-- [ ] Use a [dependency manager](https://the-turing-way.netlify.app/reproducible-research/renv/renv-package.html)
-- [ ] Pin [exact versions](https://github.com/conda/conda-lock) used to generate your environment
-
-_Optional_
-- [ ] [Containerized workflow](https://the-turing-way.netlify.app/reproducible-research/renv/renv-containers.html)
+- [ ] [Contribution guidelines](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors)
+- [ ] [Code of conduct](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-code-of-conduct-to-your-project)
@@ -466,13 +463,9 @@

FAIR assessment cards 
_Essential_  
-- [ ] [README](https://github.com/18F/open-source-guide/blob/18f-pages/pages/making-readmes-readable.md)
-- [ ] [LICENSE](https://doi.org/10.5281/zenodo.4629662)
+- [ ] [README](https://www.makeareadme.com)
+- [ ] Apply a TU Delft pre-approved [LICENSE](https://zenodo.org/records/4629635)
 - [ ] [CITATION](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files)
-
-_Recommended_  
-- [ ] Make use of [Github issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues)
-- [ ] [Code of conduct](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-code-of-conduct-to-your-project)
@@ -485,38 +478,19 @@

FAIR assessment cards 
_Essential_  
+- [ ] Source code documentation ([docstrings](https://numpydoc.readthedocs.io/en/latest/format.html))
+- [ ] Document your project dependencies
 - [ ] Installation instructions
 - [ ] User documentation
-- [ ] Developer documentation
-- [ ] Source code documentation ([docstrings](https://numpydoc.readthedocs.io/en/latest/format.html))
 
 _Recommended_  
-- [ ] Examples and tutorials (Jupyter notebooks, videos, screencasts)
-- [ ] Automate documentation building with [sphinx](https://coderefinery.github.io/sphinx-lesson/)
-- [ ] Website ([github.io pages](https://pages.github.com/), [Readthedocs](https://readthedocs.org/), [JupyterBook](https://jupyterbook.org/intro.html))
+- [ ] Developer documentation and setup
+- [ ] Examples and tutorials (e.g. Jupyter Notebooks)
 
-_Optional_  
-- [ ] Build [API reference](https://developer.lsst.io/python/numpydoc.html) from docstrings
-
-
-
-

-
-
-
-
-

Collaboration

-
-
-
_Essential_
-- [ ] Make use of [Github issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues)
-- [ ] Provide contribution [guidelines](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors)
-
-_Recommended_
-- [ ] Choose a branching model ([DCC Guides on branches](https://tu-delft-dcc.github.io/software/git/branch_management.html))
-- [ ] Make use of [issue templates](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository)
-- [ ] Provide a [Code of Conduct](https://www.contributor-covenant.org/)
-- [ ] Use [semantic versioning](https://semver.org/) for your releases
+_Optional_
+- [ ] Documentation tools ([Sphinx](https://coderefinery.github.io/documentation/sphinx/), [JupyterBook](https://jupyterbook.org/intro.html), [Quarto](https://quarto.org/docs/guide/))
+- [ ] Build an [API reference](https://developer.lsst.io/python/numpydoc.html) from docstrings
+- [ ] Hosting ([GitHub Pages](https://pages.github.com/), [Readthedocs](https://readthedocs.org/))
@@ -529,14 +503,15 @@

FAIR assessment cards 
_Essential_
-- [ ] Document verification of user installation
-- [ ] Document how users can verify the proper functioning of the software
+- [ ] Installation/execution verification
 
-_Recommended_  
-- [ ] [Defensive programming](https://swcarpentry.github.io/python-novice-inflammation/10-defensive/index.html)
+_Recommended_
+- [ ] [Defensive programming](https://swcarpentry.github.io/python-novice-inflammation/10-defensive.html)
 - [ ] Test your software with [integration tests](https://the-turing-way.netlify.app/reproducible-research/testing/testing-integrationtest.html) and [unit tests](https://the-turing-way.netlify.app/reproducible-research/testing/testing-unittest.html)
-- [ ] Make use of [Continuous Integration](https://the-turing-way.netlify.app/reproducible-research/ci/ci-options.html)
-- [ ] Code coverage check ([Codecov](https://about.codecov.io/), [Sonarcloud](https://sonarcloud.io/), [Travis](https://www.travis-ci.com/))
+- [ ] Make use of [Continuous Integration](https://coderefinery.github.io/testing/continuous-integration/) to automate testing
+
+_Optional_
+- [ ] Code coverage check (e.g. [Sonarcloud](https://sonarcloud.io/), [codecov](https://about.codecov.io))
@@ -545,18 +520,22 @@

FAIR assessment cards
-

Code quality

+

Software quality

_Essential_
-- [ ] Project [organisation](https://coderefinery.github.io/reproducible-research/organizing-projects/)
-- [ ] Record [software dependencies](https://coderefinery.github.io/reproducible-research/dependencies/)
+- [ ] [Organize](https://coderefinery.github.io/reproducible-research/organizing-projects/) your project for reproducibility
+- [ ] [Record and manage](https://coderefinery.github.io/reproducible-research/dependencies/) your software dependencies 
 
 _Recommended_
-- [ ] Follow a consistent code style, such as [PEP8 guidelines](https://realpython.com/python-pep8/)
-- [ ] Use a linter ([pylint](https://pypi.org/project/pylint/), [flake8](https://pypi.org/project/flake8/))
-- [ ] Use a formatter ([black](https://github.com/psf/black), [yapf](https://github.com/google/yapf))
+- [ ] Make [refactoring](https://refactoring.guru/refactoring) part of your workflow
 - [ ] Follow [best coding practices](https://alan-turing-institute.github.io/rse-course/html/module07_construction_and_design/index.html)
+
+_Recommended for Python_
+- [ ] Follow [PEP8 guidelines](https://realpython.com/python-pep8/)
+- [ ] Use a tool for dependency management (e.g. [poetry](https://the-turing-way.netlify.app/reproducible-research/renv/renv-package.html))
+- [ ] Use linter (e.g. [pylint](https://pypi.org/project/pylint/), [flake8](https://pypi.org/project/flake8/))
+- [ ] Use a formatter (e.g. [black](https://github.com/psf/black))
@@ -569,15 +548,17 @@

FAIR assessment cards 
_Essential_  
-- [ ] Obtain a DOI from ([Zenodo](https://zenodo.org/) or [4TU.ResearchData](https://data.4tu.nl/info/about-your-data/getting-started))
+- [ ] Obtain a DOI ([Zenodo](https://zenodo.org/) or [4TU.ResearchData](https://data.4tu.nl/info/about-your-data/getting-started))
 
 _Recommended_  
-- [ ] [Semantic versioning](https://semver.org/)
-- [ ] Tagged releases ([GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github))
+- [ ] Use [semantic versioning](https://semver.org/)
+- [ ] Create tagged releases ([GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github))
 - [ ] [CHANGELOG](https://keepachangelog.com/en/1.0.0/)
-- [ ] Upload to registry ([PyPI](https://realpython.com/pypi-publish-python-package/), [conda](https://conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html), [DockerHub](https://docs.docker.com/docker-hub/repos/))
-- [ ] [Release guide](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository)
-- [ ] [Continuous Integration](https://the-turing-way.netlify.app/reproducible-research/ci/ci-options) for build and release
+- [ ] Upload to [registry](https://github.com/NLeSC/awesome-research-software-registries) (e.g. [PyPI](https://realpython.com/pypi-publish-python-package/), [conda](https://conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html))
+- [ ] [Releasing guide](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository)
+
+_Optional_
+- [ ] [Continuous Integration](https://the-turing-way.netlify.app/reproducible-research/ci/ci-options.html) for automated build and release