Anndata #206
Workflow file for this run
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| name: Continous Integration | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build: | |
| name: Build python 🐍 package 📦 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| fetch-tags: true | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install packaging tools | |
| run : pip install build twine | |
| - name: Build package | |
| run: python -m build | |
| - name: Check package | |
| run: twine check dist/* | |
| - name: Upload distribution | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: distribution | |
| path: dist | |
| test: | |
| name: Run tests | |
| needs: build | |
| runs-on: ubuntu-latest | |
| permissions: | |
| checks: write | |
| pull-requests: write | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Dowload distribution artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: distribution | |
| path: dist | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install harissa | |
| run: pip install dist/*.whl | |
| - name: Install pytest | |
| run: pip install pytest pytest-cov | |
| - name: Run tests and coverage | |
| run: pytest | |
| - name: Publish Test Results | |
| uses: EnricoMi/publish-unit-test-result-action@v2 | |
| if: always() | |
| with: | |
| check_name: Test results (${{ matrix.python-version }}) | |
| files: report.xml | |
| - name: Renames src files name for coveralls | |
| if: always() | |
| run: sed -i -E "s/(SF:).*(\/harissa.*)/\1src\2/g" coverage.lcov | |
| - name: Upload to coveralls | |
| uses: coverallsapp/github-action@v2 | |
| if: always() | |
| with: | |
| flag-name: test-${{ matrix.python-version }} | |
| file: coverage.lcov | |
| parallel: true | |
| finish_coveralls: | |
| needs: test | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| parallel-finished: true | |
| carryforward: "test-3.8,test-3.9,test-3.10,test-3.11,test-3.12" | |
| doc: | |
| name: Generate documentation | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Dowload distribution artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: distribution | |
| path: dist | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install harissa | |
| run: pip install dist/*.whl | |
| - name: Setup documentation dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install pandoc | |
| pip install -r docs/requirements.txt | |
| - name: Build documentation | |
| run: sphinx-build docs/source html | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'documentation' | |
| path: 'html' |