Working readthedocs #2024
Workflow file for this run
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| name: CI | |
| on: | |
| - push | |
| - pull_request | |
| - workflow_dispatch | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| # ENVIRONMENT SETTINGS TO PREVENT HANGS | |
| env: | |
| OMP_NUM_THREADS: "1" | |
| MKL_NUM_THREADS: "1" | |
| OPENBLAS_NUM_THREADS: "1" | |
| VECLIB_MAXIMUM_THREADS: "1" | |
| NUMEXPR_NUM_THREADS: "1" | |
| # Agg backend is critical for headless CI | |
| MPLBACKEND: "Agg" | |
| # Prevent ProDy from checking online for updates during import | |
| PRODY_NO_UPDATE_CHECK: "1" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Cache Matplotlib | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/matplotlib | |
| key: ${{ runner.os }}-matplotlib-${{ hashFiles('environment.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-matplotlib- | |
| - name: Set up Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Verify Environment | |
| shell: bash -l {0} | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: Build & compile HPB (Linux) | |
| if: runner.os == 'Linux' | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| python setup.py build_ext --inplace --force | |
| ls -lh prody/proteins/hpb.so || { echo "hpb.so missing"; exit 1; } | |
| - name: Build & compile HPB (macOS) | |
| if: runner.os == 'macOS' | |
| shell: bash -l {0} | |
| run: | | |
| export CFLAGS="${CFLAGS} -D__NO_FLOAT16" | |
| export CPPFLAGS="${CPPFLAGS} -D__NO_FLOAT16" | |
| pushd prody/proteins/hpbmodule | |
| gfortran -O3 -fPIC -c reg_tet.f || exit 1 | |
| PYINC=$(python -c "import sysconfig; print(sysconfig.get_path('include'))") | |
| PYLIBDIR=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))") | |
| export LIBRARY_PATH="$CONDA_PREFIX/lib:$PYLIBDIR:$LIBRARY_PATH" | |
| g++ -O3 -g -fPIC -I"${PYINC}" -c hpbmodule.cpp -o hpbmodule.o || exit 1 | |
| g++ -dynamiclib -undefined dynamic_lookup \ | |
| -o hpb.so hpbmodule.o reg_tet.o \ | |
| -L"${PYLIBDIR}" -L"$CONDA_PREFIX/lib" -lgfortran || exit 1 | |
| cp hpb.so ../ | |
| popd | |
| pip install -e . | |
| python setup.py build_ext --inplace --force | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| # Warm up imports to trigger font cache build (if needed) before tests start | |
| python -c "import matplotlib.pyplot" | |
| # Run tests without debug flags | |
| pytest -v -k "not testCommandExample19 and not testCommandExample20" |