Add basic docs for the JAX support #1131
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| name: "Python ${{ matrix.python-version }} / ${{ matrix.os }} / ${{ matrix.show_build }}" | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| include: | |
| - os: ubuntu-22.04 | |
| python-version: "3.10" | |
| cxxflags: "--coverage" | |
| linkflags: "--coverage" | |
| cgaldir: "/usr/lib/x86_64-linux-gnu/cmake/CGAL/" | |
| skiptests: "expensive|medium|IMP\\.modeller\\-" | |
| show_build: Release | |
| cmake_build: Release | |
| max_checks: USAGE | |
| max_log: VERBOSE | |
| - os: ubuntu-24.04 | |
| python-version: "3.12" | |
| cxxflags: "--coverage" | |
| linkflags: "--coverage" | |
| cgaldir: "/usr/lib/x86_64-linux-gnu/cmake/CGAL/" | |
| skiptests: "expensive|medium|IMP\\.modeller\\-" | |
| show_build: Debug | |
| cmake_build: Debug | |
| max_checks: INTERNAL | |
| max_log: VERBOSE | |
| - os: ubuntu-24.04 | |
| python-version: "3.12" | |
| cxxflags: "--coverage" | |
| linkflags: "--coverage" | |
| cgaldir: "/usr/lib/x86_64-linux-gnu/cmake/CGAL/" | |
| skiptests: "expensive|medium|IMP\\.modeller\\-" | |
| show_build: Fast | |
| cmake_build: Release | |
| max_checks: NONE | |
| max_log: NONE | |
| - os: macos-latest | |
| python-version: "3.13" | |
| cxxflags: "-std=c++17 --coverage" | |
| linkflags: "--coverage" | |
| cgaldir: "/opt/homebrew/lib/cmake/CGAL/" | |
| skiptests: "expensive|medium|IMP\\.modeller\\-|IMP\\.parallel\\-test_tasks|IMP\\.parallel\\-test_startup" | |
| show_build: Release | |
| cmake_build: Release | |
| max_checks: USAGE | |
| max_log: VERBOSE | |
| steps: | |
| - uses: actions/checkout@v5 | |
| - name: Install dependencies (Linux) | |
| if: matrix.os == 'ubuntu-22.04' || matrix.os == 'ubuntu-24.04' | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -qq libboost-all-dev swig libhdf5-dev libeigen3-dev \ | |
| cmake libcgal-dev libcgal-qt5-dev libcereal-dev \ | |
| libfftw3-dev libopencv-dev libgsl-dev libann-dev \ | |
| libprotobuf-dev protobuf-compiler \ | |
| libopenmpi-dev python3-dev python3-numpy python3-protobuf \ | |
| python3-nose python3-pip python3-biopython | |
| pip3 install codecov | |
| - name: Set up Python ${{ matrix.python-version }} | |
| if: matrix.os == 'macos-latest' | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies (Mac) | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| brew install swig boost cereal cgal opencv gsl fftw eigen hdf5 protobuf | |
| pip install codecov numpy | |
| - name: Set up ccache | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| create-symlink: true | |
| - name: Set up git | |
| run: ./setup_git.py | |
| - name: Build IMP | |
| run: | | |
| mkdir build | |
| cd build | |
| PYTHONPATH=`pwd`/coverage cmake .. -DCMAKE_BUILD_TYPE="${{ matrix.cmake_build }}" -DCMAKE_CXX_FLAGS="${{ matrix.cxxflags }}" -DCGAL_DIR="${{ matrix.cgaldir }}" -DCMAKE_LINKER_FLAGS="${{ matrix.linkflags }}" -DIMP_TIMEOUT_FACTOR=4 -DIMP_MAX_CHECKS="${{ matrix.max_checks }}" -DIMP_MAX_LOG="${{ matrix.max_log }}" | |
| make -k -j 2 | |
| cd .. | |
| - name: Test IMP | |
| if: matrix.cmake_build != 'Debug' | |
| run: | | |
| cd build | |
| ../tools/coverage/setup.py | |
| PYTHONPATH=`pwd`/coverage ctest --output-on-failure -L '\-tests?-' -E "${{ matrix.skiptests }}" -T Test | |
| ctest --output-on-failure -R medium_test_standards -E 'IMP\.modeller\-' -T Test | |
| - name: Combine coverage | |
| if: matrix.cmake_build != 'Debug' | |
| run: | | |
| cd build/coverage | |
| coverage combine && coverage xml && mv coverage.xml ../.. | |
| - uses: codecov/codecov-action@v5 | |
| if: matrix.cmake_build != 'Debug' | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |