Update Python dependencies #261
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| name: CWL conformance | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| - 'lib/galaxy_test/selenium/**' | |
| pull_request: | |
| paths-ignore: | |
| - 'client/**' | |
| - 'doc/**' | |
| - 'lib/galaxy_test/selenium/**' | |
| env: | |
| GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Test | |
| if: ${{ false }} | |
| runs-on: ubuntu-latest | |
| continue-on-error: ${{ startsWith(matrix.marker, 'red') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.8'] | |
| marker: ['green', 'red and required', 'red and not required'] | |
| conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2'] | |
| services: | |
| postgres: | |
| image: postgres:13 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: postgres | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: 'galaxy root' | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '18.12.1' | |
| cache: 'yarn' | |
| cache-dependency-path: 'galaxy root/client/yarn.lock' | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get full Python version | |
| id: full-python-version | |
| shell: bash | |
| run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT | |
| - name: Cache pip dir | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} | |
| - name: Cache galaxy venv | |
| uses: actions/cache@v4 | |
| with: | |
| path: 'galaxy root/.venv' | |
| key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api | |
| - name: Run tests | |
| run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}" | |
| working-directory: 'galaxy root' | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| flags: cwl-conformance | |
| working-directory: 'galaxy root' | |
| - uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }}) | |
| path: 'galaxy root/run_cwl_tests.html' |