update_manifest_dl4miceverywhere.yml

name: Update the manifest with DL4MicEverywhere information
on:
  # At 05:30 AM of every day
  schedule:
    - cron: "30 5 * * *"
  workflow_dispatch:

jobs:
  update_manifest:
    name: Update the manifest.bioimage.io.yaml with DL4MicEverywhere information
    outputs:
      matrix: ${{ steps.create_json.outputs.matrix }}
    runs-on: ubuntu-latest
    steps:
      - name: Clone ZeroCostDL4Mic repository
        uses: actions/checkout@v4
        with:
            path: ZeroCostDL4Mic
      - name: Clone DL4MicEverywhere repository
        uses: actions/checkout@v4
        with:
            repository: HenriquesLab/DL4MicEverywhere
            path: DL4MicEverywhere
      - name: Set up Python 3.9
        uses: actions/setup-python@v5
        with:
          python-version: '3.9'
      - name: Install requirements
        working-directory: ./ZeroCostDL4Mic
        run: pip install -r Tools/CI_requirements.txt
      - name: Update the versioning on the manifest
        working-directory: ./ZeroCostDL4Mic
        run: python3 Tools/update_manifest_versioning.py
      - name: Update the DL4MicEverywhere information on the manifest
        working-directory: ./ZeroCostDL4Mic
        id: updated_notebooks
        run: |
          output=$(python3 Tools/update_manifest_dl4miceverywhere.py)
          echo "$output"
          echo "value=$output" >> $GITHUB_OUTPUT
      - if: ${{ steps.updated_notebooks.outputs.value != '' }}
        name: List and extract all notebook with new version
        id: create_json
        run: |
          echo "Start"
          files_json="{\"include\":[{\"notebook\":\""
          echo "$files_json"
          first=true
          for file in ${{ steps.updated_notebooks.outputs.value }}; do
            echo "$file was changed"
            if [ "$first" = true ]; then
              files_json+=$file
              first=false
            else
              files_json+="\"},{\"notebook\":\""$file
            fi
            echo "$files_json"
          done
          files_json+="\"}]}"
          echo "$files_json"
          echo "matrix=$files_json" >> $GITHUB_OUTPUT
          echo "END"
      - name: Commit the changes
        uses: stefanzweifel/git-auto-commit-action@v5
        with:
            repository: ./ZeroCostDL4Mic
            commit_message: GitHub Action - Update manifest with DL4MicEverywhere information
          

  config_matrix:
    if: ${{ needs.update_manifest.outputs.matrix != '' }} 
    name: Call the building and pushing, and possible update configuration
    needs: update_manifest
    strategy:
      # put fail-fast as false if you want to see all results even if one fails,
      # fail-fast is true by default
      fail-fast: false
      matrix: ${{ fromJson(needs.update_manifest.outputs.matrix) }} 
    uses: ./.github/workflows/export_notebook.yml # calls the one above ^
    with:
      notebook_name: ${{ matrix.notebook }}
    secrets: inherit