galaxy/.github/workflows/bioblend.yaml

name: BioBlend Tests
on:
  pull_request:
    paths:
      - .github/workflows/bioblend.yaml
      - lib/galaxy/schema/**
      - lib/galaxy/webapps/galaxy/api/**
      - lib/galaxy/webapps/galaxy/services/**
  workflow_dispatch:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
jobs:
  test:
    runs-on: ubuntu-latest
    services:
      postgres:
        image: postgres:17
        # Provide the password for postgres
        env:
          POSTGRES_PASSWORD: postgres
        # Set health checks to wait until postgres has started
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 5432:5432
    strategy:
      fail-fast: false
      matrix:
        tox_env: [py314]
        galaxy_python_version: ['3.10']
    steps:
      - name: Checkout Galaxy
        uses: actions/checkout@v6
        with:
          fetch-depth: 1
          path: galaxy
          persist-credentials: false
      - name: Checkout Bioblend
        uses: actions/checkout@v6
        with:
          repository: galaxyproject/bioblend
          path: bioblend
          persist-credentials: false
      - name: Calculate Python version for BioBlend from tox_env
        id: get_bioblend_python_version
        run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
      - name: Set up Python for BioBlend
        uses: actions/setup-python@v6
        with:
          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
      - name: Install uv
        uses: astral-sh/setup-uv@v7
      - name: Install tox
        run: uv tool install tox --with tox-uv
      - name: Set up Python for Galaxy
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.galaxy_python_version }}
      - name: Run tests
        env:
          PGPASSWORD: postgres
          PGPORT: 5432
          PGHOST: localhost
        run: |
          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
          createdb -U postgres galaxy
          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
          ./bioblend/run_bioblend_tests.sh -g galaxy -v python${{ matrix.galaxy_python_version }} -e ${{ matrix.tox_env }}
      - name: The job has failed
        if: ${{ failure() }}
        run: |
          cat galaxy/*.log