Same as #30 but the PR is opened from upstream repository instead of fork #3
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| # MAWS CI/CD Workflow | |
| # Runs tests on Linux with AmberTools and OpenMM across Python 3.10-3.13 | |
| # Includes optional GPU testing when self-hosted runners with GPU are available | |
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: # Allow manual trigger | |
| jobs: | |
| # ============================================================================ | |
| # Full integration tests with AmberTools (CPU) | |
| # ============================================================================ | |
| test: | |
| name: Test Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12", "3.13"] | |
| defaults: | |
| run: | |
| shell: bash -el {0} # Required for conda activate | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| activate-environment: maws | |
| auto-activate-base: false | |
| - name: Install dependencies via conda | |
| run: | | |
| conda activate maws | |
| conda install -y openmm ambertools mpmath numba pandas numpy | |
| - name: Install package and dev dependencies | |
| run: | | |
| conda activate maws | |
| pip install -e ".[dev]" | |
| - name: Verify AmberTools installation | |
| run: | | |
| conda activate maws | |
| which tleap | |
| tleap -h || echo "tleap help displayed" | |
| - name: Run tests | |
| run: | | |
| conda activate maws | |
| pytest tests/ -v --tb=short | |
| - name: Run tests with coverage | |
| if: matrix.python-version == '3.10' | |
| run: | | |
| conda activate maws | |
| pytest tests/ --cov=maws --cov-report=term-missing --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| if: matrix.python-version == '3.10' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| fail_ci_if_error: false | |
| verbose: true | |
| # ============================================================================ | |
| # Fast unit tests (no AmberTools needed) | |
| # ============================================================================ | |
| unit-tests: | |
| name: Unit Tests Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12", "3.13"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| - name: Install minimal dependencies | |
| run: | | |
| pip install numpy openmm mpmath pandas pytest pytest-cov | |
| - name: Install package | |
| run: pip install -e . | |
| - name: Run unit tests only | |
| run: | | |
| pytest tests/ -v --tb=short \ | |
| --ignore=tests/test_chain_complex.py \ | |
| --ignore=tests/test_run.py | |
| # ============================================================================ | |
| # GPU tests (only runs on self-hosted runners with NVIDIA GPU) | |
| # To enable: add a self-hosted runner with GPU and label 'gpu' | |
| # ============================================================================ | |
| gpu-test: | |
| name: GPU Test | |
| runs-on: [self-hosted, gpu] | |
| if: github.event_name == 'workflow_dispatch' || contains(github.event.head_commit.message, '[gpu]') | |
| continue-on-error: true # Don't fail the whole workflow if GPU tests fail | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Check NVIDIA GPU | |
| run: | | |
| nvidia-smi | |
| echo "CUDA devices found:" | |
| nvidia-smi --query-gpu=name,driver_version,memory.total --format=csv | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| python-version: "3.10" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| activate-environment: maws-gpu | |
| auto-activate-base: false | |
| - name: Install dependencies with CUDA support | |
| run: | | |
| conda activate maws-gpu | |
| # Install OpenMM with CUDA support | |
| conda install -y openmm cudatoolkit ambertools mpmath numba pandas numpy | |
| - name: Install package | |
| run: | | |
| conda activate maws-gpu | |
| pip install -e ".[dev]" | |
| - name: Verify CUDA platform | |
| run: | | |
| conda activate maws-gpu | |
| python -c " | |
| import openmm as mm | |
| print('Available platforms:') | |
| for i in range(mm.Platform.getNumPlatforms()): | |
| p = mm.Platform.getPlatform(i) | |
| print(f' {p.getName()}') | |
| try: | |
| cuda = mm.Platform.getPlatformByName('CUDA') | |
| print(f'CUDA platform found!') | |
| except Exception as e: | |
| print(f'CUDA not available: {e}') | |
| " | |
| - name: Run all tests including GPU | |
| env: | |
| MAWS_OPENMM_PLATFORM: CUDA | |
| run: | | |
| conda activate maws-gpu | |
| pytest tests/ -v --tb=short -m "not slow" | |
| # ============================================================================ | |
| # Linting | |
| # ============================================================================ | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install ruff | |
| run: pip install ruff | |
| - name: Run ruff check | |
| run: ruff check maws/ | |
| - name: Run ruff format check | |
| run: ruff format --check maws/ |