example-03-dependencies.md

Quarto Actions: Dependencies

If you want to execute computational content in GitHub Actions workflows, you are going to have to install the necessary software dependencies in your action.

Installing R

Add the following entry to your GitHub Actions workflow:

- uses: r-lib/actions/setup-r@v2
  with:
    r-version: '4.2.0' # The R version to download (if necessary) and use.

If you're using quarto-publish-example.yml, add those right after the # add software dependencies here comment.

Using renv to manage R packages

If you are managing your R package dependencies with renv, the following action will install the dependencies:

- uses: r-lib/actions/setup-renv@v2
  with:
    cache-version: 1

See the setup-renv documentation for how to use cache-version. See the renv documentation for how to use renv with a project.

Installing R packages manually

You can also use r-lib/actions/setup-r-dependencies@v2 to install required R packages for your content. See more about this actions at the setup-r-dependencies documentation. It can handle dependencies with a DESCRIPTION in your project, or you can also list manually what is needed. e.g

- uses: r-lib/actions/setup-r-dependencies@v2
  with:
    packages:
      any::knitr
      any::rmarkdown
      any::downlit
      any::xml2

Installing Jupyter

Add the following entry to your GitHub Actions workflow:

- uses: actions/setup-python@v4
  with:
    python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax
- run: pip install jupyter

Using requirements.txt

- uses: actions/setup-python@v4
  with:
    python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax
    cache: 'pip'
- run: pip install jupyter # (if jupyter is not part of your requirements.txt)
- run: pip install -r requirements.txt

Installing Julia

- uses: julia-actions/setup-julia@v1
- run: julia --project -e 'using Pkg; Pkg.instantiate()'