Add comprehensive test suite and coverage utilities #1
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| name: Tests and Coverage | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.11, 3.12] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache pip packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[test]" | |
| - name: Run tests with coverage | |
| run: | | |
| python -m pytest tests/ \ | |
| --cov=cellmap_flow \ | |
| --cov-report=xml \ | |
| --cov-report=term-missing \ | |
| --cov-branch \ | |
| -v | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: false | |
| coverage-report: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| if: github.event_name == 'pull_request' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[test]" | |
| pip install coverage-badge | |
| - name: Run coverage | |
| run: | | |
| python -m pytest tests/ \ | |
| --cov=cellmap_flow \ | |
| --cov-report=json \ | |
| --cov-report=html \ | |
| --cov-branch | |
| - name: Generate coverage badge | |
| run: | | |
| coverage-badge -o coverage.svg | |
| - name: Upload coverage reports as artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage-reports | |
| path: | | |
| htmlcov/ | |
| coverage.svg | |
| coverage.json | |
| retention-days: 30 | |
| coverage-comment: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| if: github.event_name == 'pull_request' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[test]" | |
| - name: Run coverage | |
| run: | | |
| python -m pytest tests/ \ | |
| --cov=cellmap_flow \ | |
| --cov-report=json | |
| - name: Coverage comment | |
| uses: py-cov-action/python-coverage-comment-action@v3 | |
| with: | |
| GITHUB_TOKEN: ${{ github.token }} |