create-documentation-pr.yml

name: create documentation PR

on:
  workflow_dispatch:
    inputs:
      version_tag:
        description: |
          The branch or tag name when generaing the QMDs. Also used for the name of the PR.
          The name of the current branch or tag is used by default
        type: string
  push:
    tags:
      - '*'

jobs:
  list:
    runs-on: ubuntu-latest
      
    outputs:
      component_matrix: ${{ steps.set_matrix.outputs.components }}
      workflow_matrix: ${{ steps.set_matrix.outputs.workflows }}
    steps:
    - uses: actions/checkout@v4

    - uses: viash-io/viash-actions/setup@v5

    - id: ns_list_components
      uses: viash-io/viash-actions/ns-list@v5
      with:
        platform: docker
        format: json
        query_namespace: ^(?!workflows)

    - id: ns_list_workflows
      uses: viash-io/viash-actions/ns-list@v5
      with:
        format: json
        query_namespace: ^workflows

    - id: set_matrix
      run: |
        echo "components=$(jq -c '[ .[] | 
          { 
            "name": .functionality.name,
            "namespace_separator": .platforms | map(select(.type == "docker"))[0].namespace_separator,
            "namespace": .functionality.namespace,
            "config": .info.config,
            "dir": .info.config | capture("^(?<dir>.*\/)").dir
          }
        ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT

        echo "workflows=$(jq -c '[ .[] | 
          { 
            "name": $config.functionality.name,
            "namespace": $config.functionality.namespace,
            "main_script": ((.info.config | capture("^(?<dir>.*\/)").dir) + "/" + (.functionality.test_resources | map(select(.type == "nextflow_script")) | unique | .[].path )),
            "config": .info.config,
            "entry": .functionality.test_resources | map(select(.type == "nextflow_script")) | .[].entrypoint
          }
        ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT

  push_documentation:
    runs-on: ubuntu-latest
    needs: [ list ]

    steps:
      - uses: actions/checkout@v4
        with:
          path: openpipelines

      - uses: actions/checkout@v4
        with:
          repository: openpipelines-bio/website
          path: website
          token: ${{ secrets.GTHB_PAT }}

      - uses: viash-io/viash-actions/setup@v5
      
      - name: Get tag to use
        id: get_tag
        run: |
          INPUT_TAG="${{ github.event.inputs.version_tag }}"
          TAG_OR_BRANCH_NAME=${INPUT_TAG:-"${{ github.ref_name }}"}
          echo "tag=$TAG_OR_BRANCH_NAME" >> $GITHUB_OUTPUT

      - uses: viash-io/viash-actions/pro/generate-documentation-qmd@v5
        with:
          project_directory: openpipelines
          src: ./
          output_dir: ../website/components/
          dest_path: "{type}s/{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          ref: "${{ steps.get_tag.outputs.tag }}"

      - name: Create Pull Request
        env:
          GITHUB_TOKEN: ${{ secrets.GTHB_PAT }}
        working-directory: website
        run: |
          git config user.name github-actions
          git config user.email github-actions@github.com
          git add .
          git checkout -B "release-${{ steps.get_tag.outputs.tag }}"
          git commit -m "OpenPipelines release ${{ steps.get_tag.outputs.tag }}"
          git push --set-upstream origin "release-${{ steps.get_tag.outputs.tag }}"
          gh pr create --title "Openpipeline release ${{ steps.get_tag.outputs.tag }}" --base main --head "release-${{ steps.get_tag.outputs.tag }}" --body ""