Update CI workflow configuration #103
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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: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| swig \ | |
| cmake \ | |
| dssp \ | |
| build-essential \ | |
| curl \ | |
| git \ | |
| python3-dev \ | |
| gcc \ | |
| gfortran \ | |
| libblas-dev \ | |
| liblapack-dev \ | |
| libhdf5-dev \ | |
| libnetcdf-dev \ | |
| libfftw3-dev \ | |
| libopenmm-dev \ | |
| libboost-all-dev \ | |
| libxml2-dev \ | |
| libxslt1-dev \ | |
| zlib1g-dev \ | |
| libjpeg-dev \ | |
| libpng-dev \ | |
| libfreetype6-dev \ | |
| libatlas-base-dev \ | |
| pkg-config | |
| - name: Set up conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.8" | |
| channels: conda-forge,defaults | |
| channel-priority: strict | |
| activate-environment: proteinflex-env | |
| auto-activate-base: false | |
| auto-update-conda: true | |
| - name: Install bioinformatics dependencies | |
| shell: bash -el {0} | |
| run: | | |
| # Install bioinformatics packages from conda-forge | |
| conda install -y -c conda-forge mdtraj=1.9.7 openmm=7.7.0 prody=2.0.0 | |
| - name: Set up Python dependencies | |
| shell: bash -el {0} | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| # Install scientific dependencies | |
| pip install numpy==1.23.5 scipy==1.9.3 pandas==1.5.3 matplotlib==3.6.2 biopython==1.80 | |
| # Install ML dependencies | |
| pip install torch==1.13.1+cpu --extra-index-url https://download.pytorch.org/whl/cpu | |
| pip install transformers==4.25.1 tokenizers==0.13.2 | |
| pip install google-generativeai==0.2.0 | |
| # Install testing dependencies | |
| pip install pytest==7.1.2 pytest-cov==3.0.0 coverage==6.5.0 flake8==5.0.4 | |
| pip install pytest-mock==3.10.0 pytest-asyncio==0.20.3 pytest-timeout==2.1.0 | |
| pip install pytest-xdist==3.1.0 mock==5.0.1 pytest-env==0.8.1 pytest-randomly==3.12.0 | |
| # Install package in editable mode | |
| pip install -e . | |
| - name: Run tests | |
| shell: bash -el {0} | |
| env: | |
| PYTHONPATH: ${{ github.workspace }} | |
| OPENMM_CPU_THREADS: 1 | |
| PROTEINFLEX_TEST_MODE: 1 | |
| PYTHONWARNINGS: ignore::DeprecationWarning | |
| TRANSFORMERS_OFFLINE: 1 | |
| CUDA_VISIBLE_DEVICES: "" | |
| OMP_NUM_THREADS: 1 | |
| MKL_NUM_THREADS: 1 | |
| GOOGLE_API_KEY: ${{ secrets.GOOGLE_API_KEY }} | |
| run: | | |
| # Run tests with coverage, skipping API tests if no key available | |
| if [ -z "$GOOGLE_API_KEY" ]; then | |
| pytest tests/ -v -m "not requires_api" --cov=proteinflex --cov-report=xml --import-mode=importlib | |
| else | |
| pytest tests/ -v --cov=proteinflex --cov-report=xml --import-mode=importlib | |
| fi | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| - name: Check code style | |
| shell: bash -el {0} | |
| run: | | |
| 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 conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.8" | |
| channels: conda-forge,defaults | |
| channel-priority: strict | |
| activate-environment: proteinflex-env | |
| auto-activate-base: false | |
| auto-update-conda: true | |
| - name: Install dependencies | |
| shell: bash -el {0} | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel build | |
| # Install scientific dependencies | |
| pip install numpy==1.23.5 scipy==1.9.3 pandas==1.5.3 matplotlib==3.6.2 biopython==1.80 | |
| - name: Build package | |
| shell: bash -el {0} | |
| run: | | |
| # Build package | |
| python -m build | |
| python setup.py bdist_wheel | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ |