publish_latest_to_zenodo.yml

name: 3. Publish latest release to Zenodo

on:
  workflow_dispatch:
  schedule:
  - cron: "30 06 15 * *"

jobs:
  publish-zenodo:
    runs-on: ubuntu-latest  
    env: 
      ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          path: wikipathways-data-release
          fetch-depth: 0
          ref: main

      - name: Checkout pyzenodo4wpdata
        uses: actions/checkout@v4
        with:
          repository: wikipathways/pyzenodo4wpdata
          path: pyzenodo4wpdata
          fetch-depth: 0
          ref: main
  
      - name: Publish to Zenodo
        run: |
          # Find latest 8-digit release number from dir names under wikipathways-data-release
          RELEASE=$(ls -d wikipathways-data-release/* | grep -o '[0-9]\{8\}' | sort -n | tail -1)
          echo "RELEASE set to $RELEASE"
          # Copy files from pyzenodo4wpdata
          cp pyzenodo4wpdata/pyzenodo4wpdata.py .
          cp pyzenodo4wpdata/meta-template.json .
          # Publish GMT to Zenodo
          for f in wikipathways-data-release/$RELEASE/gmt/*.gmt; do
            if [ -f "$f" ]; then
              echo "$f"
              python pyzenodo4wpdata.py ${ZENODO_TOKEN} meta-template.json $RELEASE $f
            fi
          done
          # Publish GPML to Zenodo
          for f in wikipathways-data-release/$RELEASE/gpml/*.zip; do
            if [ -f "$f" ]; then
              echo "$f"
              python pyzenodo4wpdata.py ${ZENODO_TOKEN} meta-template.json $RELEASE $f
            fi
          done