Same as #30 but the PR is opened from upstream repository instead of fork

.github/workflows/ci.yml

@@ -0,0 +1,208 @@
+# 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/

.gitignore

@@ -42,18 +42,6 @@ htmlcov/
 *.mo
 *.pot
 
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
 docs/_build/
@@ -104,7 +92,9 @@ dmypy.json
 cython_debug/
 
 #MAWS pdf files
-maws_*.pdb
 .maws_cache/
 *.in
-*.mdp
+*.mdp
+*.log
+*.lib
+# We have to correct all this before release