SDEV-4155 - switch to source.displayName for Pharmacogenomic filterin… #390
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 4 | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install .[test] | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 graphkb --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - name: Check with black | |
| run: | | |
| pip install black | |
| black --check -S -l 100 graphkb tests | |
| - name: Test with pytest | |
| run: | | |
| pip list | |
| pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov graphkb --cov-report term --cov-report xml --durations 10 -vv | |
| env: | |
| GRAPHKB_USER: ${{ secrets.GKB_TEST_USER }} | |
| GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }} | |
| EXCLUDE_INTEGRATION_TESTS: 0 | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: junit/test-results-${{ matrix.python-version }}.xml | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: always() | |
| - name: Update code coverage report to CodeCov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| env_vars: OS,PYTHON | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| if: matrix.python-version == 3.9 |