galaxy/.github/workflows/integration.yaml

name: Integration
on:
  push:
    paths-ignore:
      - 'client/**'
      - 'doc/**'
      - 'lib/galaxy_test/selenium/**'
      - 'packages/**'
  pull_request:
    paths-ignore:
      - 'client/**'
      - 'doc/**'
      - 'lib/galaxy_test/selenium/**'
      - 'packages/**'
  schedule:
    # Run at midnight UTC every Tuesday
    - cron: '0 0 * * 2'
  workflow_dispatch:
env:
  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
  GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1'
  GALAXY_DEPENDENCIES_INSTALL_HTCONDOR: '1'
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
permissions: {}
jobs:
  prepare-mulled-cache:
    name: Prepare mulled resolution cache
    runs-on: ubuntu-latest
    steps:
      - name: Select weekly cache
        run: echo "MULLED_CACHE_WEEK=$(date -u +%G-%V)" >> "$GITHUB_ENV"
      - name: Restore Biocontainers repository index
        id: restore-mulled-cache
        uses: actions/cache/restore@v6.1.0
        with:
          key: biocontainers-repository-index-${{ env.MULLED_CACHE_WEEK }}
          path: '${{ runner.temp }}/mulled-resolution-seed'
      - name: Check out Galaxy for mulled-cache
        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
        uses: actions/checkout@v7.0.1
        with:
          path: 'galaxy cache source'
          persist-credentials: false
      - name: Install uv
        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
        uses: astral-sh/setup-uv@v9.0.0
        with:
          python-version: '3.10'
      - name: Fetch Biocontainers repository index
        id: fetch-mulled-cache
        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
        continue-on-error: true
        env:
          SEED_DIRECTORY: '${{ runner.temp }}/mulled-resolution-seed'
        run: |
          uv tool run --from './galaxy cache source/packages/tool_util' mulled-cache \
              --namespace biocontainers \
              --output "$SEED_DIRECTORY/biocontainers.json"
      - name: Save Biocontainers repository index
        if: steps.restore-mulled-cache.outputs.cache-hit != 'true' && steps.fetch-mulled-cache.outcome == 'success'
        uses: actions/cache/save@v6.1.0
        with:
          key: biocontainers-repository-index-${{ env.MULLED_CACHE_WEEK }}
          path: '${{ runner.temp }}/mulled-resolution-seed'
      - name: Create fallback seed
        if: steps.fetch-mulled-cache.outcome == 'failure'
        env:
          SEED_DIRECTORY: '${{ runner.temp }}/mulled-resolution-seed'
        run: |
          echo '::warning::Could not index the biocontainers namespace, integration tests run without a seeded mulled resolution cache'
          mkdir -p "$SEED_DIRECTORY"
          echo '{"namespace":"biocontainers","repositories":[]}' > "$SEED_DIRECTORY/biocontainers.json"
      - name: Upload mulled resolution cache seed
        uses: actions/upload-artifact@v7
        with:
          name: mulled-resolution-cache-seed
          path: '${{ runner.temp }}/mulled-resolution-seed/biocontainers.json'
          retention-days: 1

  test:
    name: Test
    needs: prepare-mulled-cache
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ['3.10']
        chunk: ['0', '1', '2', '3']
    steps:
      - if: github.event_name == 'schedule'
        run: |
          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
          # --cov=lib line-traces a live Galaxy for the whole job, so integration
          # coverage is collected on this weekly run only.
          echo "GALAXY_TEST_COVERAGE=1" >> $GITHUB_ENV
          # Skip outputs_to_working_directory: true in integration tests, doesn't work with pulsar
          # echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
      - name: Prune unused docker image, volumes and containers
        run: docker system prune -a -f
      - name: Clean dotnet folder for space
        run: rm -Rf /usr/share/dotnet
      - name: Install packages
        # ffmpeg: ffprobe needed by media datatypes
        run: sudo apt-get update && sudo apt-get -y install ffmpeg
      - name: Setup Minikube
        uses: medyagh/setup-minikube@latest
        with:
          driver: none
          kubernetes-version: '1.28.0'
      - name: Check pods
        run: kubectl get pods -A
      - uses: actions/checkout@v7.0.1
        with:
          path: 'galaxy root'
          persist-credentials: false
      - name: Install uv
        uses: astral-sh/setup-uv@v9.0.0
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install Python
        run: uv python install
      - name: Download mulled resolution cache seed
        uses: actions/download-artifact@v8
        with:
          name: mulled-resolution-cache-seed
          path: '${{ runner.temp }}/mulled-resolution-seed'
      - name: Install Apptainer's singularity
        uses: './galaxy root/.github/actions/install_apptainer'
      - name: Run tests
        env:
          GALAXY_TEST_MULLED_RESOLUTION_CACHE_SEED: '${{ runner.temp }}/mulled-resolution-seed/biocontainers.json'
          GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_DATA_DIR: '${{ runner.temp }}/mulled-resolution-cache/data'
          GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_LOCK_DIR: '${{ runner.temp }}/mulled-resolution-cache/locks'
        run: |
          . .ci/minikube-test-setup/start_services.sh
          ./run_tests.sh -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
        working-directory: 'galaxy root'
      - uses: codecov/codecov-action@v7.0.0
        if: github.event_name == 'schedule'
        with:
          flags: integration
          working-directory: 'galaxy root'
      - uses: actions/upload-artifact@v7
        if: failure()
        with:
          name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
          path: 'galaxy root/run_integration_tests.html'