[WIP] Implement Sample Sheets #235
Workflow file for this run
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| 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 | |
| # 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: [py313] | |
| galaxy_python_version: ["3.8"] | |
| steps: | |
| - name: Checkout Galaxy | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| path: galaxy | |
| - name: Checkout Bioblend | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: galaxyproject/bioblend | |
| path: bioblend | |
| - name: Cache pip dir | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-cache-${{ matrix.tox_env }} | |
| - name: Calculate Python version for BioBlend from tox_env | |
| id: get_bioblend_python_version | |
| run: echo "bioblend_python_version=$(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@v5 | |
| with: | |
| python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }} | |
| - name: Install tox | |
| run: | | |
| python3 -m pip install --upgrade pip setuptools | |
| python3 -m pip install 'tox>=1.8.0' | |
| - name: Set up Python for Galaxy | |
| uses: actions/setup-python@v5 | |
| 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 |