Put partition command in correct method call #4108
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| name: Test | |
| on: | |
| # Building on pull-requests, manual dispatch, and pushes to main; but restricting | |
| # publishing only to main pushes and manual dispatch with `if`s in specific steps. | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: "true" | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install | |
| run: pip install .[test] | |
| - name: Run unit tests | |
| id: runtests | |
| timeout-minutes: 20 | |
| run: | | |
| PYTHONPATH=$PWD/gnomad_methods:$PWD/seqr-loading-pipelines \ | |
| coverage run -m pytest -n auto test --junitxml=test-execution.xml | |
| rc=$? | |
| coverage xml | |
| echo "rc=$rc" >> $GITHUB_OUTPUT | |
| - name: 'Save coverage report as an Artifact' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: ./coverage.xml | |
| - name: 'Save execution report as an Artifact' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: execution-report | |
| path: ./test-execution.xml | |
| - name: "Upload coverage reports to Codecov" | |
| uses: codecov/[email protected] | |
| with: | |
| files: ./coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Fail if unit tests are not passing | |
| if: ${{ steps.runtests.outputs.rc != 0}} | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| core.setFailed('Unittests failed with rc = ${{ steps.runtests.outputs.rc }}') | |
| sonarqube: | |
| name: SonarQube scan | |
| runs-on: ubuntu-latest | |
| needs: test | |
| environment: production | |
| if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis | |
| # Download the coverage report artifact | |
| - name: 'Download coverage and execution report' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: '*-report' | |
| # Perform the SonarQube scan | |
| - uses: sonarsource/sonarqube-scan-action@master | |
| env: | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }} | |
| # Optional: Fail the job if Quality Gate is red | |
| # If you wish to fail your job when the Quality Gate is red, uncomment the | |
| # following lines. This would typically be used to fail a deployment. | |
| # - uses: sonarsource/sonarqube-quality-gate-action@master | |
| # timeout-minutes: 5 | |
| # env: | |
| # SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} |