CI #35
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: [ master ] | |
| schedule: | |
| - cron: '0 0 * * 0,3' | |
| workflow_dispatch: | |
| jobs: | |
| build_wheel: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: [3.8, 3.9, '3.10', '3.11'] | |
| exclude: | |
| - os: macos-latest | |
| python-version: '3.11' | |
| env: | |
| GEANT4_VERSION: 'v11.1.1' | |
| ITK_VERSION: 'v5.2.1' | |
| steps: | |
| - name: Checkout github repo | |
| uses: actions/checkout@v3 | |
| - name: Checkout submodules | |
| run: | | |
| export GIT_SSL_NO_VERIFY=1 | |
| git submodule update --init --recursive | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Get OS version | |
| id: get-os-version | |
| run: | | |
| if [ ${{ matrix.os }} == "ubuntu-latest" ]; then | |
| varOS=`cat /etc/os-release | grep "VERSION=" | grep -oP '(?<=\").*?(?=\")'` | |
| varOS=($varOS) | |
| echo "release=${varOS[0]}" >> $GITHUB_OUTPUT | |
| else | |
| varOS=`sw_vers | grep "ProductVersion:"` | |
| varOS="${varOS#*:}" | |
| echo "release=${varOS:1}" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Cache modules | |
| id: cache_opengate_core_dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/software | |
| key: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build3 | |
| restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build3 | |
| - name: Create opengate Wheel | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| if [ ${{ matrix.python-version }} == "3.9" ]; then | |
| rm -rf $GITHUB_WORKSPACE/opengate/tests/data | |
| cp $GITHUB_WORKSPACE/.git/modules/gam-tests/data/HEAD $GITHUB_WORKSPACE/opengate/tests/ | |
| pip install wheel | |
| python setup.py sdist bdist_wheel | |
| mv dist dist_opengate | |
| fi | |
| - name: Create opengate_core Wheel Linux | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| if [ ${{ matrix.python-version }} == "3.8" ]; then | |
| export PYTHONFOLDER="cp38-cp38" | |
| elif [ ${{ matrix.python-version }} == "3.9" ]; then | |
| export PYTHONFOLDER="cp39-cp39" | |
| elif [ ${{ matrix.python-version }} == "3.10" ]; then | |
| export PYTHONFOLDER="cp310-cp310" | |
| elif [ ${{ matrix.python-version }} == "3.11" ]; then | |
| export PYTHONFOLDER="cp311-cp311" | |
| fi | |
| mkdir -p $HOME/software | |
| docker run --rm -e "PYTHONFOLDER=${PYTHONFOLDER}" -v $GITHUB_WORKSPACE:/home tbaudier/opengate_core:${{ env.GEANT4_VERSION }} /home/.github/workflows/createWheelLinux.sh | |
| ls wheelhouse | |
| rm -rf dist | |
| mv wheelhouse dist | |
| sudo chown -R runner:docker dist | |
| if [ ${{ matrix.python-version }} == "3.9" ]; then | |
| ls -lrt . | |
| ls -lrt dist/ | |
| ls -lrt dist_opengate/ | |
| mv dist_opengate/* dist/ | |
| fi | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| if: matrix.os == 'macos-latest' | |
| with: | |
| auto-update-conda: true | |
| activate-environment: opengate_core | |
| python-version: ${{ matrix.python-version }} | |
| - name: Create opengate_core Wheel Mac | |
| if: matrix.os == 'macos-latest' | |
| shell: bash -l {0} | |
| run: | | |
| brew update | |
| rm -rf /usr/local/bin/python3.11-config /usr/local/bin/2to3-3.11 /usr/local/bin/idle3.11 /usr/local/bin/pydoc3.11 /usr/local/bin/python3.11 | |
| rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3 | |
| brew install --force --verbose --overwrite \ | |
| ccache \ | |
| fftw \ | |
| libomp \ | |
| xquartz \ | |
| xerces-c \ | |
| wget | |
| brew uninstall --ignore-dependencies libxext | |
| brew uninstall --ignore-dependencies libx11 | |
| export LDFLAGS="-L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/llvm/include -fopenmp" | |
| conda info | |
| conda list | |
| which python | |
| python --version | |
| export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH" | |
| pip install wget colored | |
| pip install cibuildwheel==2.12.0 | |
| conda install -c conda-forge qt==5.15.6 | |
| mkdir -p $HOME/software | |
| if [ "${{ steps.cache_opengate_core_dependencies.outputs.cache-hit }}" != 'true' ]; then | |
| cd $HOME/software | |
| mkdir geant4 | |
| cd geant4 | |
| mkdir src bin data | |
| git clone --branch $GEANT4_VERSION https://github.com/Geant4/geant4.git --depth 1 src | |
| cd bin | |
| cmake -DCMAKE_CXX_FLAGS=-std=c++17 \ | |
| -DGEANT4_INSTALL_DATA=OFF \ | |
| -DGEANT4_INSTALL_DATADIR=$HOME/software/geant4/data \ | |
| -DGEANT4_USE_QT=ON \ | |
| -DGEANT4_USE_OPENGL_X11=ON \ | |
| -DGEANT4_BUILD_MULTITHREADED=ON \ | |
| -DGEANT4_USE_GDML=ON \ | |
| ../src | |
| make -j4 | |
| cd $HOME/software | |
| mkdir itk | |
| cd itk | |
| mkdir src bin | |
| git clone --branch $ITK_VERSION https://github.com/InsightSoftwareConsortium/ITK.git --depth 1 src | |
| cd bin | |
| cmake -DCMAKE_CXX_FLAGS=-std=c++17 \ | |
| -DBUILD_TESTING=OFF \ | |
| -DITK_USE_FFTWD=ON \ | |
| -DITK_USE_FFTWF=ON \ | |
| -DITK_USE_SYSTEM_FFTW:BOOL=ON \ | |
| ../src | |
| make -j4 | |
| fi | |
| cd $GITHUB_WORKSPACE | |
| ls /usr/local/miniconda/envs/opengate_core/plugins/platforms | |
| source $HOME/software/geant4/bin/geant4make.sh | |
| export CMAKE_PREFIX_PATH=$HOME/software/geant4/bin:$HOME/software/itk/bin/:${CMAKE_PREFIX_PATH} | |
| cd core | |
| mkdir opengate_core/plugins | |
| mkdir opengate_core/plugins/miniconda | |
| rm -rf dist | |
| if [ ${{ matrix.python-version }} == "3.8" ]; then | |
| export CIBW_BUILD="cp38-macosx_x86_64" | |
| elif [ ${{ matrix.python-version }} == "3.9" ]; then | |
| export CIBW_BUILD="cp39-macosx_x86_64" | |
| elif [ ${{ matrix.python-version }} == "3.10" ]; then | |
| export CIBW_BUILD="cp310-macosx_x86_64" | |
| fi | |
| export CIBW_BEFORE_BUILD="python -m pip install colored" | |
| python -m cibuildwheel --output-dir dist | |
| cd dist | |
| cd ../.. | |
| mv core/dist . | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| publish_wheel: | |
| runs-on: ubuntu-latest | |
| needs: [build_wheel] | |
| steps: | |
| - name: Checkout github repo | |
| uses: actions/checkout@v3 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Separate the wheels | |
| run: | | |
| mkdir dist_opengate_core dist_opengate | |
| mv dist/opengate_core-* dist_opengate_core/ | |
| mv dist/opengate-* dist_opengate/ | |
| - name: Publish to PyPI opengate_core | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/') | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_OPENGATE_CORE }} | |
| packages_dir: dist_opengate_core/ | |
| skip_existing: true | |
| - name: Publish to PyPI opengate | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/') | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_OPENGATE }} | |
| packages_dir: dist_opengate/ | |
| skip_existing: true | |
| test_wheel: | |
| runs-on: ${{ matrix.os }} | |
| needs: [build_wheel] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: [3.8, 3.9, '3.10', '3.11'] | |
| exclude: | |
| - os: macos-latest | |
| python-version: '3.11' | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Run tests | |
| run: | | |
| if [ ${{ matrix.python-version }} == "3.8" ]; then | |
| export PYTHONFOLDER="cp38-cp38" | |
| elif [ ${{ matrix.python-version }} == "3.9" ]; then | |
| export PYTHONFOLDER="cp39-cp39" | |
| elif [ ${{ matrix.python-version }} == "3.10" ]; then | |
| export PYTHONFOLDER="cp310-cp310" | |
| pip install --pre itk | |
| elif [ ${{ matrix.python-version }} == "3.11" ]; then | |
| export PYTHONFOLDER="cp311-cp311" | |
| pip install --pre itk | |
| fi | |
| if [ ${{ matrix.os }} == "ubuntu-latest" ]; then | |
| export OSNAME="manylinux" | |
| pip install torch --extra-index-url https://download.pytorch.org/whl/cpu | |
| elif [ ${{ matrix.os }} == "macos-latest" ]; then | |
| export OSNAME="macosx" | |
| pip install torch | |
| fi | |
| pip install gaga_phsp | |
| pip install garf | |
| pip install dist/opengate_core-*-${PYTHONFOLDER}-${OSNAME}*_x86_64.whl | |
| pip install dist/opengate-*.whl | |
| export GIT_SSL_NO_VERIFY=1 | |
| if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then | |
| path=`opengate_tests_utils -p site_packages` | |
| export LD_LIBRARY_PATH="${path}/opengate_core.libs":${LD_LIBRARY_PATH} | |
| path=`opengate_tests_utils -p libG4processes` | |
| export LD_PRELOAD=${path}:${LD_PRELOAD} | |
| path=`opengate_tests_utils -p libG4geometry` | |
| export LD_PRELOAD=${path}:${LD_PRELOAD} | |
| fi | |
| OutputTest=$(opengate_tests) | |
| echo "$OutputTest" | |
| OutputTest=$(echo "$OutputTest" | tail -1) | |
| if [ "$OutputTest" != "True" ]; then | |
| exit -1 | |
| else | |
| exit 0 | |
| fi |