roxygenize.yml

# The purpose of this action is to run `document()` of the roxygen2 package on each commit.
# If new documentation was generated, it will automatically add a commit to the current branch.
# This has the same effect as running `document()` locally, but
#  * ensures it cannot be forgotten
#  * saves setting up the development environment locally, which is especially useful for new contributors.
#
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  pull_request:
    paths: ["R/**", ".github/workflows"]

name: Document

jobs:
  document:
    runs-on: ubuntu-latest # self-hosted
    env:
      GITHUB_PAT: ${{ secrets.TOKEN }}
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          # extra token required to trigger github actions again on commit
          token: ${{ secrets.TOKEN }} # BOT_GH_TOKEN

      - name: Update system dependencies
        run: |
          sudo apt-get update && sudo apt-get install  \
          libcurl4-openssl-dev -y

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install pak
        run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')"

      #- name: Install SpatialExperiment
      # run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"

      - name: Install Devtools
        run: Rscript -e "pak::pkg_install('devtools')"

      - name: Install SpatialExperiment
        run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          dependencies: '"hard"' # do not install suggests
          extra-packages: any::roxygen2
          needs: roxygen2

      - name: Document
        run: roxygen2::roxygenise()
        shell: Rscript {0}

      - uses: stefanzweifel/git-auto-commit-action@v4
        with:
          commit_message: Roxygenize