ci.yml

# 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/