count-git-contributions.yml

name: cronjob for counting git contributions and filing a PR with results

# Run every Monday at 8:00 UTC
# On Monday, we count git contributions
# But we can also manually trigger this
on:
  schedule:
    - cron: "0 14 * * MON"
  workflow_dispatch:
permissions:
  pull-requests: write
jobs:
  file-count-contributions-pr:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    container:
      image: rocker/tidyverse:4.4

    # We want to count the contributions to the dev branch
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
        with:
          ref: "dev"
          fetch-depth: 0

      - name: Configure git
        run: |
          git config --global --add safe.directory "$GITHUB_WORKSPACE"
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"

      # We need this package for one of the notebooks run via the shell script below
      - name: Install yaml R package
        run: Rscript -e "install.packages('yaml')"

      # Rerun the module we want new results for
      - name: Rerun count-contributions module
        run: |
          bash analyses/count-contributions/run-count-contributions.sh

      # Upload the manuscript YAML as an artifact
      - name: Upload metadata YAML artifact
        uses: actions/upload-artifact@v4
        with:
          name: manuscript_metadata
          path: analyses/count-contributions/results/metadata.yaml

      # Upload the author information as an artifact
      - name: Upload author information TSV artifact
        uses: actions/upload-artifact@v4
        with:
          name: author_information
          path: analyses/count-contributions/author_information.tsv

      # Create a pull request with the updated results
      - name: Create PR with updated contribution module
        uses: peter-evans/create-pull-request@v6
        with:
          token: ${{ secrets.GH_TOKEN }}
          commit-message: Rerun count-contributions analysis module
          signoff: false
          branch: auto_count_contributions
          delete-branch: true
          title: 'GHA: Updated git contribution stats'
          body: |
            ### Description

            This PR auto-generated from GitHub Actions rerunning `analyses/count-contributions`
 
            ### Instruction for reviewers

            Review the updates in `analyses/count-contributions/results/` for accuracy
          reviewers: $GITHUB_ACTOR

  file-metadata-yaml-pr:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    needs: file-count-contributions-pr

    # We want to add the updated metadata to the manuscript repo
    steps:
      - name: Checkout manuscript repository
        uses: actions/checkout@v4
        with:
          repository: d3b-center/OpenPedCan-manuscript
      
      - name: Configure git
        run: |
          git config --global --add safe.directory "$GITHUB_WORKSPACE"
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"

      # Set up directories to be able to receive artifacts
      # Note, You can not overwrite an existing file with an artifact,
      #  so this step also removes existing files.
      - name: Directory setup
        run: |
          mkdir -p submission_info/
          rm -f submission_info/author_information.tsv
          rm content/metadata.yaml

      - name: Download the metadata artifact
        uses: actions/download-artifact@v3
        with:
          name: manuscript_metadata
          path: content


      - name: Download the author information artifact
        uses: actions/download-artifact@v3
        with:
          name: author_information
          path: submission_info


      # Create a pull request with the updated results
      - name: Create PR with updated manuscript metadata YAML
        uses: peter-evans/create-pull-request@v6
        with:
          token: ${{ secrets.GH_TOKEN }}
          commit-message: Update manuscript metadata
          signoff: false
          branch: auto_author_order
          delete-branch: true
          title: 'GHA: Updated author order'
          body: |
            ### Description

            This PR auto-generated from GitHub Actions workflow that counts git contributions and sets author order accordingly in the `AlexsLemonade/OpenPBTA-analysis` repo.
            See [the relevant module](https://github.com/d3b-center/OpenPedCan-analysis/tree/dev/analyses/count-contributions) for more info.
 
            ### Instruction for reviewers

            Review the updates in `content/metadata.yaml` and `submission_info/author_information.tsv` for accuracy.

          reviewers: $GITHUB_ACTOR