bump version to 3.4.6 #35
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Python | |
| on: | |
| push: | |
| branches: [ main, python ] | |
| paths: | |
| - 'python-kalign/**' | |
| - 'lib/**' | |
| - 'CMakeLists.txt' | |
| - 'pyproject.toml' | |
| - '.github/workflows/python.yml' | |
| pull_request: | |
| branches: [ main ] | |
| paths: | |
| - 'python-kalign/**' | |
| - 'lib/**' | |
| - 'CMakeLists.txt' | |
| - 'pyproject.toml' | |
| - '.github/workflows/python.yml' | |
| workflow_dispatch: | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 black isort mypy | |
| - name: Lint with flake8 | |
| run: | | |
| flake8 python-kalign --count --select=E9,F63,F7,F82 --show-source --statistics | |
| flake8 python-kalign --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Check formatting with black | |
| run: | | |
| black --check --diff python-kalign/ | |
| - name: Check import sorting with isort | |
| run: | | |
| isort --check-only --diff python-kalign/ | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install system dependencies (Ubuntu) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libomp-dev cmake | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install libomp cmake | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest pytest-cov pytest-benchmark numpy | |
| - name: Build and install package | |
| run: | | |
| python -m pip install -e . | |
| - name: Test with pytest | |
| run: | | |
| pytest tests/python/ -v --cov=kalign --cov-report=xml --cov-report=term-missing | |
| - name: Upload coverage to Codecov | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage.xml | |
| flags: python | |
| name: codecov-umbrella | |
| build-test: | |
| name: Build and test package | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install system dependencies (Ubuntu) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libomp-dev cmake | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install libomp cmake | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install build twine | |
| - name: Build package | |
| run: | | |
| python -m build | |
| - name: Check package | |
| run: | | |
| twine check dist/* | |
| - name: Test installation from wheel | |
| run: | | |
| python -m pip install dist/*.whl | |
| python -c "import kalign; print(f'kalign {kalign.__version__} installed successfully')" | |
| - name: Test basic functionality | |
| run: | | |
| python -c " | |
| import kalign | |
| sequences = ['ATCGATCG', 'ATCGTCG', 'ATCGATCG'] | |
| aligned = kalign.align(sequences, seq_type='dna') | |
| assert len(aligned) == 3 | |
| print('✓ Basic alignment test passed') | |
| " |