check_r_dependencies.yml

name: Check R dependencies

on:
  schedule:
    # * is a special character in YAML so you have to quote this string
    - cron:  '0 0 * * 0'
  workflow_run:
    workflows:
      - 'Run Tests'
    types:
      - completed
    branches:
      - 'main'

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

permissions:
  contents: write
  pull-requests: write

jobs:
  check-r-dependencies:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3
      with:
        fetch-depth: 1

    - name: Check for available updates
      run: |
        for REQUIREMENTS in $(ls -1 docker/*/r_requirements.txt); do
          IMAGE=$(echo ${REQUIREMENTS} | sed 's:^docker/::' | sed 's:/.*::')
          docker pull -q singlecellopenproblems/${IMAGE}
          PKG_CHANGED=$(
            docker run -t --rm --user=root \
              -v $(pwd):/usr/src/singlecellopenproblems \
              singlecellopenproblems/${IMAGE} \
              Rscript /usr/src/singlecellopenproblems/scripts/upgrade_renv.R \
              /usr/src/singlecellopenproblems/${REQUIREMENTS} | \
              tee /dev/stderr | \
              tail -n 1 | \
              sed 's-::-/-g'
          )
          git diff --exit-code || break
          PKG_CHANGED=""
        done
        echo "PKG_CHANGED=$(echo ${PKG_CHANGED} | sed 's/@/ to /')" >> $GITHUB_ENV
        echo "UPDATE_BRANCH_NAME=dependencies/r/${PKG_CHANGED}" >> $GITHUB_ENV

    - name: Create Pull Request
      if: >-
        env.PKG_CHANGED != ''
      uses: peter-evans/create-pull-request@v4
      with:
        branch: ${{ env.UPDATE_BRANCH_NAME }}
        delete-branch: true
        base: main
        labels: dependencies,r
        title: "Update ${{ env.PKG_CHANGED }}"
        committer: "openproblems-bio <singlecellopenproblems@protonmail.com>"
        author: "openproblems-bio <singlecellopenproblems@protonmail.com>"
        commit-message: "Update ${{ env.PKG_CHANGED }} # ci skip"
        draft: true