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Guide to sesync-ci/*-lesson Repositories

The lessons maintained by the SESYNC-CI organization are held in separate repositories that nonetheless share common files. The tree shown below shows files from the lesson-style repository that are shared (merged) into all lessons. Except for README.md and docs/_config.yml, these files shall only be modified in the lesson-style repository.

lesson-style.git
├── bin/
│   ├── build_slides.R
│   └── build_slides.py
├── CONTRIBUTING.md
├── data -> /nfs/public-data/training
├── docs/
│   ├── _config.yml
│   ├── course/
│   │   ├── archive.html
│   │   └── index.md
│   ├── css/
│   │   ├── default.css
│   │   ├── slideshow.css
│   │   └── static.css
│   ├── Gemfile
│   ├── Gemfile.lock
│   ├── _includes/
│   │   ├── body.html
│   │   ├── head.html
│   │   └── subst_content.html
│   ├── index.md
│   ├── instructor/
│   │   └── index.md
│   ├── _layouts/
│   │   ├── archive.html
│   │   ├── course.html
│   │   ├── default.html
│   │   ├── instructor.html
│   │   └── slides.html
│   └── slides/
│       └── index.md
├── Makefile
└── README.md

Each lesson repository will include the above files in addition to the topical material, carefully arranged within all or some of the following files and folders:

*-lesson.git
├── README.md
├── ...
└── docs/
    ├── _posts/
    ├── _slides/
    ├── _slides_Rmd/ | _slides_pmd/ | _slides_md/
    ├── images/
    └── _config.yml

Note that README.md and docs/_config.yml occur in both; the versions/templates in lesson-style include instructions on which parts to modify once brought into a *-lesson repository to avoid merge conflicts.

For a lesson written in RMarkdown, place .Rmd files within docs/_slides_Rmd; knitted slides will be generated within docs/_slides. Likewise, any slides to be processed by Pweave go in docs/_slides_pmd. If a lesson is written purely in Markdown, the slides may reside in docs/_slides, but a lesson that combines Markdown slides with processed slides should include doc/_slides_md and let the build process populate docs/_slides.

Data for the lesson goes in the public-data/training folder on SESYNC's research storage server, which is symlinked from the data folder in each lesson. References to data in lesson code shall be via the relative path data/. Figures produced during build and any external images go in docs/images. Archived versions of the lesson go in docs/_posts.

Including a handouts.Rproj makes it convenient to start an R session with the appropriate working directory, and will be included in the [handouts] associated with each lesson. All additional handouts (including data) must be listed in the docs/_config.yml.

The Makefile includes targets for building and publishing lessons:

  • make slides to run the bin/build_slides.* scripts that populate docs/_slides
  • make lesson makes the slides and publishes to GitHub
  • make archive $DATE copies the lesson as generated on GitHub into the docs/_posts archive.

Creating a new lesson

Create a new, public repository owned by the SESYNC-CI organization: use a short name, provide a description that can be exported as a human readable lesson title (e.g. on SESYNC's lessons tab), and do not include a README.

Locally clone lesson-style repository into a suitably named *-lesson folder, rename the branch and remote, and checkout a new master:

git clone [email protected]:SESYNC-ci/lesson-style.git $LESSON-lesson
cd $LESSON-lesson
git remote set-url origin [email protected]:SESYNC-ci/$LESSON-lesson.git
git push

Everything above is standardized across lessons, the following is where the real work begins! First, go to the lesson repository's GitHub settings and select master/docs as the GitHub Pages source. Configure README.md by commiting the following to the README.md file, after replacing $LESSON with the new lesson's name.

[lesson]: https://sesync-ci.github.io/$LESSON-lesson
[slideshow]: https://sesync-ci.github.io/$LESSON-lesson/slides

Configure the lesson by setting the following variables in the # Site section of the docs/_config.yml YAML file.

  • title: a lesson title
  • handouts: the list of handouts, e.g. worksheets and data
  • tag: the release version associated with the handouts.zip attached to a release, if any
  • lesson: the number of the lesson in a workshop setting
  • instructor: who will give the lesson in a workshop setting
  • authors: the list of contributors

Always create the docs/_slides folder, but develop content within one of the following folders as appropriate:

  • docs/_slides_md for markdown (.md)
  • docs/_slides_Rmd for RMarkdown (.Rmd)
  • docs/_slides_pmd for Pweave (.pmd)

Each file within one of these folders becomes a vertical stack of slides in a Reveal.js presentation: use "===" on it's own line to indicate a slide break. Vertical stacks are concatenated horizontally in the order supplied by the slide_sorter array in docs/_config.yml.

Preview a Lesson

Each lesson is a Jekyll site, automatically deployed by GitHub when pushed but also possible to serve up (with a little work) locally. The following instructions work with a *-lesson repo open as a project on https://rstudio.sesync.org.

From a terminal, execute:

make preview

This builds a static Jekyll site if any of the site content (e.g. the docs/_slides folder) has been updated since the last site build. To view the page in a browser, use the servr R package:

servr::httd('docs/_site', port = 4000, initpath = 'instructor', daemon = TRUE)

Other valid initpath arguments are course, slides, or nothing. If port 4000 is not available, you'll have to dig into the Makefile and manually build the Jekyll site with a different "baseurl".

Versioning and Releases

A lesson should be archived after any event in which it is presented—either in a workshop or à la carte setting. The archive is a built (i.e. processed into HTML) page copied into docs/_posts. Given a date for the post, the archive target in the Makefile will download from docs/course/archive.html from GitHub, non-course archives should be downloaded manually. There are two "versioning" variables to set in docs/_config.yml before archiving:

  • tag refers to a release of the lesson, along with associated data and worksheets
  • styleurl refers to a release of lesson-style

The corresponing releases must exist:

  • The lesson's repository needs a release corresponding to tag that includes any data and worksheets in a handouts.zip "binary" attachment.
  • After updating the styleurl, create the release in lesson-style before archiving any lessons

Upstream

The repository lesson-style is intended to be upstream of all *-lesson repositories, but configuration as such must be achieved in a local clone (i.e. not on GitHub). This upstream remote will be configured on the first call to make slides.

To merge changes made within the lesson-style repository into a lesson, run git pull upstream master from the master branch. The upstream commits may not have a shared history with the master branch; it is okay to use --allow-unrelated-histories. Modifications to the upstream branch shall be meant for all lessons. A change to docs/_layouts/default.html, for example, should be commited to the upstream branch and pushed to the master branch of the upstream remote (i.e. to the lesson-style repository on GitHub):

git checkout upstream
git add docs/_layouts/default.html
git commit
git push upstream HEAD:master

Prefer to make changes directly to the lesson-style.