Check R dependencies #478
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| 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 <[email protected]>" | |
| author: "openproblems-bio <[email protected]>" | |
| commit-message: "Update ${{ env.PKG_CHANGED }} # ci skip" | |
| draft: true |