GaCDI/.github/workflows/ci.yml at main · goeckslab/GaCDI · GitHub

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name: CI

on:
  push:
    branches: [main, manifest_tool]
  pull_request:

jobs:
  pytest:
    name: Unit tests (mcdi)
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: cli_tools/mcdi
    strategy:
      matrix:
        python-version: ["3.10", "3.12"]
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install
        run: python -m pip install -e '.[dev]'
      - name: Run tests
        run: pytest -q -m "not network"

  planemo-lint:
    name: Lint Galaxy tools
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install planemo
        run: python -m pip install planemo
      - name: Lint manifest_gdc
        run: planemo lint tools/manifest_gdc
      - name: Lint manifest_downloader
        run: planemo lint tools/manifest_downloader

  planemo-test-manifest-downloader:
    name: Test Galaxy tool (manifest_downloader)
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install planemo
        run: python -m pip install planemo

      - name: Read version from package __init__.py
        id: version
        run: |
          VERSION=$(grep -m1 '^__version__' cli_tools/mcdi/mcdi/__init__.py | sed -E 's/__version__ = "(.*)"/\1/')
          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"

      # Built locally and never pushed: this only has to exist for this job's
      # own `planemo test --docker` step to resolve the tag manifest_downloader.xml
      # references. The real, published image is built and pushed by
      # containers.yml, only on merge to main.
      - name: Build mcdi image (local only, not pushed)
        run: |
          docker build \
            --build-arg MCDI_BUILD=${{ github.sha }} \
            -t quay.io/goeckslab/mcdi:${{ steps.version.outputs.version }} \
            cli_tools/mcdi

      - name: Test
        run: planemo test --docker tools/manifest_downloader

      - name: Upload test report
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: manifest-downloader-test-report
          path: tool_test_output.html
          if-no-files-found: warn