style: fix formatting in geometry.py #49
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| name: CI | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| # Cancel in-progress runs for the same branch | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| # Dependency review for PRs (security check) | |
| dependency-review: | |
| if: github.event_name == 'pull_request' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Dependency Review | |
| uses: actions/dependency-review-action@v4 | |
| with: | |
| fail-on-severity: high | |
| # Deny licenses that are incompatible with MIT | |
| deny-licenses: GPL-3.0, AGPL-3.0 | |
| # Test with native C++ module | |
| test-native: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ['3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Eigen (Ubuntu) | |
| if: matrix.os == 'ubuntu-latest' | |
| run: sudo apt-get update && sudo apt-get install -y libeigen3-dev | |
| - name: Install Eigen (macOS) | |
| if: matrix.os == 'macos-latest' | |
| run: brew install eigen | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' # Cache pip dependencies | |
| - name: Install dependencies | |
| run: | | |
| pip install "gemmology-cdl-parser @ git+https://github.com/gemmology-dev/cdl-parser.git" | |
| pip install -e ".[dev]" -v | |
| - name: Verify native module loaded | |
| run: | | |
| python -c " | |
| from crystal_geometry import get_backend, get_backend_info | |
| info = get_backend_info() | |
| print(f'Backend: {info[\"backend\"]}') | |
| print(f'Native available: {info.get(\"native_available\", False)}') | |
| print(f'Native version: {info.get(\"native_version\", \"N/A\")}') | |
| print(f'Native functions: {info.get(\"native_functions\", [])}') | |
| assert get_backend() == 'native', f'Expected native backend, got {get_backend()}' | |
| print('Native module verified!') | |
| " | |
| - name: Run tests with coverage | |
| run: pytest --cov=src/crystal_geometry --cov-report=xml --cov-report=term-missing -v | |
| - name: Upload coverage to Codecov | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| flags: native | |
| name: native-ubuntu-py311 | |
| fail_ci_if_error: false # Don't fail if Codecov is down | |
| token: ${{ secrets.CODECOV_TOKEN }} # Optional for public repos | |
| - name: Run benchmarks | |
| run: python benchmarks/numpy_vs_native.py | |
| # Test pure Python fallback (no Eigen) | |
| test-python-fallback: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install without native module | |
| run: | | |
| pip install "gemmology-cdl-parser @ git+https://github.com/gemmology-dev/cdl-parser.git" | |
| # Install without building native module (skip cmake) | |
| pip install numpy scipy pytest pytest-cov ruff mypy | |
| pip install -e . --no-build-isolation --config-settings=cmake.define.SKIP_NATIVE=ON || pip install -e . | |
| env: | |
| CMAKE_ARGS: "-DSKIP_BUILD=ON" | |
| - name: Verify Python fallback | |
| run: | | |
| python -c " | |
| from crystal_geometry import get_backend | |
| backend = get_backend() | |
| print(f'Backend: {backend}') | |
| print('Fallback working!') | |
| " | |
| - name: Run tests with coverage | |
| run: pytest --cov=src/crystal_geometry --cov-report=xml --cov-report=term-missing -v | |
| - name: Upload coverage to Codecov | |
| if: matrix.python-version == '3.12' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| flags: python-fallback | |
| name: fallback-py312 | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| # Lint and type check | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| pip install "gemmology-cdl-parser @ git+https://github.com/gemmology-dev/cdl-parser.git" | |
| pip install -e ".[dev]" --no-build-isolation || pip install numpy scipy ruff mypy | |
| - name: Lint with Ruff | |
| run: ruff check . --output-format=github | |
| - name: Check formatting with Ruff | |
| run: ruff format --check . | |
| - name: Type check with mypy | |
| run: mypy src/ | |
| # Coverage gate - enforce 80% minimum | |
| coverage-gate: | |
| needs: [test-native, test-python-fallback] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| pip install "gemmology-cdl-parser @ git+https://github.com/gemmology-dev/cdl-parser.git" | |
| # Install build deps and dev dependencies first, then package | |
| pip install scikit-build-core pybind11 numpy scipy pytest pytest-cov | |
| pip install -e . --no-build-isolation | |
| env: | |
| CMAKE_ARGS: "-DSKIP_BUILD=ON" | |
| - name: Run tests with coverage | |
| # Target: 80%, Current threshold: 60% (incrementally increasing) | |
| run: pytest --cov=src/crystal_geometry --cov-report=term-missing --cov-fail-under=60 | |
| - name: Coverage report | |
| run: | | |
| echo "## Coverage Report" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "Current threshold: **60%** (Target: 80%)" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "Uncovered modules to prioritize:" >> $GITHUB_STEP_SUMMARY | |
| echo "- \`_optim.py\` - optimization functions" >> $GITHUB_STEP_SUMMARY | |
| echo "- \`geometry.py\` - core geometry" >> $GITHUB_STEP_SUMMARY | |
| echo "- \`twins/generators.py\` - twin generation" >> $GITHUB_STEP_SUMMARY |