Increased visibility of variant callers's "Pass" or "Filtered" on SNVs and SVs variants pages (both RD and cancer variants) #21053
Workflow file for this run
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| name: Run tests and push coverage to Codecov | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| # Cache package installation step to speed up the following step | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('requirements-dev.txt') }} | |
| - name: Install deps | |
| run: | | |
| pip install --upgrade --upgrade-strategy eager -r requirements-dev.txt -r requirements.txt -e . | |
| pip check | |
| test: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| group: [1, 2, 3, 4, 5, 6, 7, 8] | |
| mongodb-version: ['7'] | |
| steps: | |
| - name: Start MongoDB | |
| uses: supercharge/mongodb-github-action@1.10.0 | |
| with: | |
| mongodb-version: ${{ matrix.mongodb-version }} | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| # Cache package installation step to speed up the following step | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('requirements-dev.txt') }} | |
| - name: Install the HTML 2 PDF renderer | |
| run: sudo apt-get update || true && sudo apt-get install -y wkhtmltopdf | |
| - name: Run pytest | |
| run: pytest --cov --test-group-count 8 --test-group=${{ matrix.group }} --test-group-random-seed=12345 --rootdir=/home/runner/work/scout | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage${{ matrix.group }} | |
| path: .coverage | |
| include-hidden-files: true | |
| coverage: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Install deps | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install coverage | |
| - name: Download all artifacts | |
| # Download and combine coverage1, coverage2, etc. | |
| uses: actions/download-artifact@v4 | |
| - name: Run coverage | |
| run: | | |
| coverage combine coverage*/.coverage* | |
| coverage report | |
| coverage xml | |
| - uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |