Merge pull request #35 from bcgsc/bugfix/SDEV-4409_ACYP2_pharmacogeno… #120
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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: | |
| branches: | |
| - main | |
| - develop | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install -e .[test] # coverage reports need -e to capture properly | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - name: Check with black | |
| run: | | |
| pip install black | |
| black --check -S -l 100 pori_python tests | |
| - name: Full Tests with pytest | |
| run: | | |
| pip list | |
| pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov pori_python --cov-report term --cov-report xml | |
| env: | |
| IPR_USER: ${{ secrets.IPR_TEST_USER }} | |
| IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }} | |
| GRAPHKB_USER: ${{ secrets.GKB_TEST_USER }} | |
| GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }} | |
| # SDEV-3381 - Turn off integration tests temporarily, till efficiency is increased | |
| # turn on integration tests for one python version only | |
| EXCLUDE_INTEGRATION_TESTS: ${{ matrix.python-version != '3.11' }} | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: pytest-results-${{ 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: matrix.python-version == 3.9 | |
| - 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 |