openpipeline_docs/.github/workflows/generate-reference.yml at c45c35918d9561975f48f6e3329f95d37dc37248 · openpipelines-bio/openpipeline_docs · GitHub

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name: Generate reference

# Auto-generates the reference documentation for the whole OpenPipeline
# ecosystem from source. This repo pulls each package, runs the Viash
# documentation generator over its configs, and opens a PR with the result —
# so the reference can never drift from the code, and no package repo needs a
# workflow of its own.
#
# Requires repo secret GTHB_PAT: a GitHub PAT with viash-hub pro access (and
# read access to any private package repo).

on:
  workflow_dispatch:
    inputs:
      ref:
        description: "Branch or tag to generate from for every package (default: main)."
        type: string
        default: main
  schedule:
    - cron: "0 6 * * 1" # Mondays 06:00 UTC

permissions:
  contents: write
  pull-requests: write

jobs:
  generate:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout docs
        uses: actions/checkout@v4
        with:
          path: openpipeline_docs
          token: ${{ secrets.GTHB_PAT }}

      # Package checkouts pass the PAT so private repos resolve and so the same
      # token is available for a re-added private package later.
      - name: Checkout openpipeline
        uses: actions/checkout@v4
        with: { repository: openpipelines-bio/openpipeline, ref: "${{ inputs.ref || 'main' }}", path: openpipeline, token: "${{ secrets.GTHB_PAT }}" }
      - name: Checkout openpipeline_spatial
        uses: actions/checkout@v4
        with: { repository: openpipelines-bio/openpipeline_spatial, ref: "${{ inputs.ref || 'main' }}", path: openpipeline_spatial, token: "${{ secrets.GTHB_PAT }}" }
      - name: Checkout openpipeline_qc
        uses: actions/checkout@v4
        with: { repository: openpipelines-bio/openpipeline_qc, ref: "${{ inputs.ref || 'main' }}", path: openpipeline_qc, token: "${{ secrets.GTHB_PAT }}" }
      - name: Checkout openpipeline_composed
        uses: actions/checkout@v4
        with: { repository: openpipelines-bio/openpipeline_composed, ref: "${{ inputs.ref || 'main' }}", path: openpipeline_composed, token: "${{ secrets.GTHB_PAT }}" }

      - uses: viash-io/viash-actions/setup@v6

      # Two passes per package (the proven openpipeline→website recipe): modules
      # first (clean:true wipes stale pages), then workflows (clean:false appends).
      # Both land under reference/<package>/<namespace>/<name>.qmd. A single
      # combined query returned zero components, so mirror the working split.
      - name: Generate — openpipeline (modules)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline
          query: '^(?!workflows|test_workflows)'
          output_dir: ../openpipeline_docs/reference/openpipeline/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: true
      - name: Generate — openpipeline (workflows)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline
          query: '^workflows'
          output_dir: ../openpipeline_docs/reference/openpipeline/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: false

      - name: Generate — openpipeline_spatial (modules)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline_spatial
          query: '^(?!workflows|test_workflows)'
          output_dir: ../openpipeline_docs/reference/openpipeline_spatial/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: true
      - name: Generate — openpipeline_spatial (workflows)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline_spatial
          query: '^workflows'
          output_dir: ../openpipeline_docs/reference/openpipeline_spatial/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: false

      - name: Generate — openpipeline_qc (modules)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline_qc
          query: '^(?!workflows|test_workflows)'
          output_dir: ../openpipeline_docs/reference/openpipeline_qc/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: true
      - name: Generate — openpipeline_qc (workflows)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline_qc
          query: '^workflows'
          output_dir: ../openpipeline_docs/reference/openpipeline_qc/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: false

      - name: Generate — openpipeline_composed (modules)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline_composed
          query: '^(?!workflows|test_workflows)'
          output_dir: ../openpipeline_docs/reference/openpipeline_composed/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: true
      - name: Generate — openpipeline_composed (workflows)
        uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
        with:
          project_directory: openpipeline_composed
          query: '^workflows'
          output_dir: ../openpipeline_docs/reference/openpipeline_composed/
          dest_path: "{namespace}/{name}.qmd"
          viash_pro_token: ${{ secrets.GTHB_PAT }}
          tools_version: main_build
          clean: false

      - name: Open PR
        working-directory: openpipeline_docs
        env:
          GITHUB_TOKEN: ${{ secrets.GTHB_PAT }}
        run: |
          git config user.name github-actions
          git config user.email github-actions@github.com
          git add reference
          if git diff --cached --quiet; then
            echo "Reference already up to date — nothing to propose."
            exit 0
          fi
          BRANCH="reference/update-${{ inputs.ref || 'main' }}"
          git checkout -B "$BRANCH"
          git commit -m "Regenerate reference from ${{ inputs.ref || 'main' }}"
          git push --force-with-lease --set-upstream origin "$BRANCH"
          gh pr create --title "Regenerate reference (${{ inputs.ref || 'main' }})" \
            --base main --head "$BRANCH" \
            --body "Auto-generated from all five packages' Viash configs. Do not hand-edit \`reference/<package>/\`." \
            || echo "PR already open for $BRANCH; branch updated."