Complete fixture-based testing infrastructure to reduce database test runtime to <6 seconds #1919
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| name: CI | |
| on: | |
| - push | |
| - pull_request | |
| - workflow_dispatch | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: test | |
| auto-update-conda: true | |
| channels: conda-forge | |
| architecture: ${{ runner.arch }} | |
| - name: Install deps | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test | |
| conda install --yes -c conda-forge compilers gfortran | |
| conda install --yes \ | |
| "numpy" \ | |
| "pyparsing<=3.1.1" \ | |
| scipy nose pytest requests \ | |
| pdbfixer mdtraj openmm | |
| conda install -c bioconda --yes clustalw | |
| pip install mmtf-python scikit-learn | |
| - name: Build & compile HPB (Linux) | |
| if: runner.os == 'Linux' | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test | |
| pip install -e . | |
| python setup.py build_ext --inplace --force | |
| echo "Verifying hpb.so file properties on Linux:" | |
| ls -lh prody/proteins/hpb.so || { echo "hpb.so not found on Linux!"; exit 1; } | |
| file prody/proteins/hpb.so || { echo "file command failed for hpb.so on Linux!"; exit 1; } | |
| ldd prody/proteins/hpb.so || { echo "ldd failed or found issues on Linux!"; exit 1; } | |
| - name: Build & compile HPB (macOS) | |
| if: runner.os == 'macOS' | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test | |
| echo "Debugging environment variables before compilation:" | |
| echo "PATH: $PATH" | |
| echo "CONDA_PREFIX: $CONDA_PREFIX" | |
| echo "LIBRARY_PATH: $LIBRARY_PATH" | |
| echo "CPATH: $CPATH" | |
| echo "DYLD_LIBRARY_PATH: $DYLD_LIBRARY_PATH" | |
| export CFLAGS="${CFLAGS} -D__NO_FLOAT16" | |
| export CPPFLAGS="${CPPFLAGS} -D__NO_FLOAT16" | |
| pushd prody/proteins/hpbmodule | |
| echo "Contents of hpbmodule directory:" | |
| ls -l | |
| echo "Attempting Fortran compilation..." | |
| gfortran -O3 -fPIC -c reg_tet.f || { echo "Fortran compilation of reg_tet.f failed!"; exit 1; } | |
| echo "reg_tet.f compiled successfully to reg_tet.o." | |
| ls -lh reg_tet.o | |
| file reg_tet.o | |
| PYINC=$(python -c "import sysconfig; print(sysconfig.get_path('include'))") | |
| PYLIBDIR=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))") | |
| echo "Python Include Dir (PYINC): ${PYINC}" | |
| echo "Python Lib Dir (PYLIBDIR): ${PYLIBDIR}" | |
| [ -d "${PYINC}" ] || { echo "Python Include Dir '${PYINC}' does not exist!"; exit 1; } | |
| [ -d "${PYLIBDIR}" ] || { echo "Python Lib Dir '${PYLIBDIR}' does not exist!"; exit 1; } | |
| export LIBRARY_PATH="$CONDA_PREFIX/lib:$PYLIBDIR:$LIBRARY_PATH" | |
| echo "Attempting C++ compilation..." | |
| g++ -O3 -g -fPIC -I"${PYINC}" -c hpbmodule.cpp -o hpbmodule.o || { echo "C++ compilation of hpbmodule.cpp failed!"; exit 1; } | |
| echo "hpbmodule.cpp compiled successfully to hpbmodule.o." | |
| ls -lh hpbmodule.o | |
| file hpbmodule.o | |
| echo "Attempting HPB linking for macOS..." | |
| g++ -dynamiclib \ | |
| -undefined dynamic_lookup \ | |
| -o hpb.so hpbmodule.o reg_tet.o \ | |
| -L"${PYLIBDIR}" -L"$CONDA_PREFIX/lib" -lgfortran || { echo "HPB shared library linking failed!"; exit 1; } | |
| echo "hpb.so linked successfully." | |
| echo "Verifying hpb.so file properties (macOS):" | |
| ls -lh hpb.so || { echo "hpb.so not found after linking!"; exit 1; } | |
| file hpb.so || { echo "File type check failed for hpb.so!"; exit 1; } | |
| otool -L hpb.so || { echo "otool -L failed or found issues for hpb.so! This usually means it's not a valid Mach-O binary."; exit 1; } | |
| cp hpb.so ../ | |
| popd | |
| pip install -e . | |
| python setup.py build_ext --inplace --force | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test | |
| pytest |