fix: Implement EnhancedSampling class and fix import error #139
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| name: CI | |
| on: | |
| push: | |
| branches: [main, feature/*] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10.13' | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| swig \ | |
| cmake \ | |
| libopenmm-dev \ | |
| dssp \ | |
| build-essential \ | |
| curl \ | |
| git \ | |
| python3-dev \ | |
| gcc \ | |
| gfortran \ | |
| libblas-dev \ | |
| liblapack-dev \ | |
| libhdf5-dev \ | |
| libnetcdf-dev | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest pytest-cov | |
| # Install build dependencies first | |
| pip install setuptools wheel Cython==0.29.36 | |
| # Install core dependencies | |
| pip install numpy==1.23.5 scipy==1.9.3 | |
| # Install OpenMM first | |
| pip install openmm==8.0.0 | |
| # Install mdtraj dependencies | |
| pip install pandas networkx joblib | |
| # Now install mdtraj | |
| pip install --no-cache-dir mdtraj==1.9.7 | |
| # Install remaining requirements | |
| pip install -r requirements.txt | |
| # Install package in development mode with explicit path | |
| PYTHONPATH=$PYTHONPATH:$(pwd) pip install -e . | |
| - name: Run tests | |
| run: | | |
| # Run tests from project root with proper Python path | |
| PYTHONPATH=$PYTHONPATH:$(pwd) python -m pytest \ | |
| tests/test_dynamics.py \ | |
| tests/test_mutation_analysis.py \ | |
| -v --cov=models | |
| - name: Check code style | |
| run: | | |
| pip install flake8 | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| flake8 . --count --exit-zero --max-complexity=10 \ | |
| --max-line-length=80 --statistics | |
| build: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10.13' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install build wheel | |
| - name: Build package | |
| run: | | |
| python -m build | |
| python setup.py bdist_wheel | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ |