Merge pull request #78 from Clinical-Genomics/pass_through_unannotated #29
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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') }} }} | |
| - name: Install deps | |
| run: | | |
| pip install --upgrade --upgrade-strategy eager -e . | |
| pip check | |
| test: | |
| needs: 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') }} | |
| - name: Install pytest | |
| run: pip install pytest pytest-cov | |
| - name: Run pytest | |
| run: pytest --cov --rootdir=/home/runner/work/stranger | |
| - 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 }} |