Use GitHub actions with R Markdown and Distill

How can you automatically render README, Distill website…

Etienne Bacher
2021-03-19

The preview image comes from: https://github.com/marketplace/actions/cancel-workflow-action

Sometimes, it is useful to automatically render an R Markdown document or a website, made with distill for example. In this post, I will present you two cases in which I use GitHub Actions to automatically do that.

Render a README

One of my GitHub repos is a list of JavaScript libraries that have been adapted in R. You can find the repo here. I wanted this list to be easy to update, so that it can be done on GitHub directly. The idea is that when I (or someone else) find a JavaScript library that has been adapted into an R package, I add it to a CSV file on GitHub. The problem is that this CSV file is then used into an R Markdown file, that creates a clean README with all the information.

Without GitHub Actions, in addition to modify the CSV file, I would have to clone the repo, open it in RStudio, render the README, and push it back on GitHub.

But this task is repetitive: apart from the details I add to the CSV file, it can be automated. This is where GitHub Actions comes into play. The idea is that you create a .yml file that contains the R code you want to run to render the README. This is what mine looks like:

on:
  push:
    branches: master

name: Render README

jobs:
  render:
    name: Render README
    runs-on: macOS-latest
    steps:
      - uses: actions/checkout@v2
      - uses: r-lib/actions/setup-r@v1
      - uses: r-lib/actions/setup-pandoc@v1
      - name: Install rmarkdown
        run: Rscript -e 'install.packages("rmarkdown")'
      - name: Render README
        run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")'
      - name: Commit results
        run: |
          git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
          git push origin || echo "No changes to commit"

The first two parts are quite self-explanatory:

The third part needs a bit more details. There are some parts that I just copied and pasted from the R actions repository, but basically you can see that first it initiates R and pandoc (setup-r@v1, setup-pandoc@v1). Then, I run an R script to install the rmarkdown package and I use it to render the Rmd file to create README.md.

Last but not least, GitHub Actions rendered the README, but the changes are not on the repo yet. Hence, the last step is to commit the changes with a message and to push them on the master branch. Now, every time I change the CSV file on the master branch, the README will be automatically rendered (after a few minutes, since all the actions have to run first).

I said this was the .yaml file I use on my repo, but I lied a bit. Actually, for my list of JavaScript libraries to be up-to-date, I also need to scrape the htmlwidgets gallery once in a while. Hence, I use cron to run GitHub Actions every Sunday night at 23:59. See the documentation to know how to format your schedule. Finally, here’s the .yaml file I use:

on:
  push:
    branches: master
  schedule:
    - cron: '59 23 * * 0'

name: Render README

jobs:
  render:
    name: Render README
    runs-on: macOS-latest
    steps:
      - uses: actions/checkout@v2
      - uses: r-lib/actions/setup-r@v1
      - uses: r-lib/actions/setup-pandoc@v1
      - name: Install rmarkdown
        run: Rscript -e 'install.packages("rmarkdown")'
      - name: Render README
        run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")'
      - name: Commit results
        run: |
          git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
          git push origin || echo "No changes to commit"

Render a Distill website

To automatically render your distill website on every push on master branch, the logic is very similar. In my .yml file, there are two main differences.

The first one is that I need to install more packages to render my distill website. Some will be essential for everyone (e.g distill) but other packages won’t be (e.g postcards).

The second one is more tricky, but could be useful for several people. Before using distill, I used blogdown. For some reasons (and mostly because distill is much easier in my opinion), I switched to distill. However, this switch changed a few URLs addresses, for my posts for instance. Therefore, I needed a _redirects file to, well, redirect the old URLs to the new ones and prevent 404 errors. The _redirects file needs to be in the _site folder, because it is the folder that is used by Netlify to build the site. The problem here is that this folder is deleted and re-generated every time rmarkdown::render_site() is called, i.e every time the website is locally built. Therefore, the _redirects file couldn’t just stay there. I had to add it manually after every build.

The solution to that is to automate this in GitHub Actions. After having rendered the website, I just copy _redirects from its location on the repo to the _site folder. Now, every time I change something on the master branch, the distill website is rebuilt, and then the _redirects file is added.

One drawback though: since these files are changed on GitHub only, the first thing you have to do when opening your site project in RStudio is to pull the changes (or, like me, you will struggle with merge conflicts).

To finish this post, here’s the .yml file for my distill website:

on:
  push:
    branches: master

name: Render & Deploy Site

jobs:
  build:
    runs-on: macOS-latest
    steps:
      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-r@master

      - uses: r-lib/actions/setup-pandoc@master

      - name: Install dependencies
        run: |
          install.packages("rmarkdown")
          install.packages("distill")
          install.packages("postcards")
          install.packages("devtools")
          install.packages("fs")
          devtools::install_github("etiennebacher/ebmisc")
        shell: Rscript {0}

      - name: Render Site
        run: Rscript -e 'rmarkdown::render_site(encoding = "UTF-8")'
      - name: Copy redirects
        run: Rscript -e 'fs::file_copy("_redirects", "_site/_redirects")'
      - name: Commit results
        run: |
          git add -A
          git commit -m 'Rebuild site' || echo "No changes to commit"
          git push origin || echo "No changes to commit"

Corrections

If you see mistakes or want to suggest changes, please create an issue on the source repository.

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/etiennebacher/personal_website_distill, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".

Citation

For attribution, please cite this work as

Bacher (2021, March 19). Etienne Bacher: Use GitHub actions with R Markdown and Distill. Retrieved from https://www.etiennebacher.com/posts/2021-03-19-use-github-actions-with-r-markdown-and-distill/

BibTeX citation

@misc{bacher2021use,
  author = {Bacher, Etienne},
  title = {Etienne Bacher: Use GitHub actions with R Markdown and Distill},
  url = {https://www.etiennebacher.com/posts/2021-03-19-use-github-actions-with-r-markdown-and-distill/},
  year = {2021}
}