Carm contrib #2100
Workflow file for this run
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| 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-12, windows-latest] | |
| python-version: [3.8, 3.9, '3.10', '3.11'] | |
| env: | |
| GEANT4_VERSION: 'v11.2.1' | |
| ITK_VERSION: 'v5.2.1' | |
| steps: | |
| - name: Checkout github repo | |
| uses: actions/checkout@v4 | |
| - name: Checkout submodules | |
| shell: bash -l {0} | |
| run: | | |
| if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then | |
| export GIT_SSL_NO_VERIFY=1 | |
| git submodule update --init --recursive | |
| elif [[ ${{ matrix.os }} == "macos-12" ]]; then | |
| export GIT_SSL_NO_VERIFY=1 | |
| git submodule update --init --recursive | |
| else | |
| set "GIT_SSL_NO_VERIFY=1" | |
| git submodule update --init --recursive | |
| fi | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Get OS version | |
| id: get-os-version | |
| shell: bash -l {0} | |
| run: | | |
| if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then | |
| varOS=`cat /etc/os-release | grep "VERSION=" | grep -oP '(?<=\").*?(?=\")'` | |
| varOS=($varOS) | |
| echo "release=${varOS[0]}" >> $GITHUB_OUTPUT | |
| elif [[ ${{ matrix.os }} == "macos-12" ]]; then | |
| varOS=`sw_vers | grep "ProductVersion:"` | |
| varOS="${varOS#*:}" | |
| echo "release=${varOS:1}" >> $GITHUB_OUTPUT | |
| else | |
| varOS=`windows` | |
| echo "release=${varOS}" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Cache modules | |
| id: cache_opengate_core_dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/software | |
| key: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build1 | |
| restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build1 | |
| - 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 build | |
| python -m build | |
| 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@v3 | |
| if: (matrix.os == 'macos-12') || (matrix.os == 'windows-latest') | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| activate-environment: opengate_core | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up Homebrew | |
| if: matrix.os == 'macos-12' | |
| id: set-up-homebrew | |
| uses: Homebrew/actions/setup-homebrew@master | |
| - name: Create opengate_core Wheel Mac | |
| if: matrix.os == 'macos-12' | |
| shell: bash -l {0} | |
| run: | | |
| brew install python@3.12 || true | |
| brew link --overwrite python@3.12 | |
| #brew update | |
| #rm -rf /usr/local/bin/python3.1*-config /usr/local/bin/2to3-3.1* /usr/local/bin/idle3.1* /usr/local/bin/pydoc3.1* /usr/local/bin/python3.1* | |
| #rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3 | |
| brew install --force --verbose --overwrite \ | |
| ccache \ | |
| fftw \ | |
| libomp \ | |
| xquartz \ | |
| xerces-c \ | |
| wget | |
| brew uninstall --ignore-dependencies libxext | |
| brew uninstall --ignore-dependencies libx11 | |
| export LDFLAGS="-L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/llvm/include -fopenmp" | |
| conda info | |
| conda list | |
| which python | |
| python --version | |
| export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH" | |
| pip install wget colored | |
| pip install cibuildwheel==2.17.0 | |
| 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_USE_SYSTEM_EXPAT=OFF \ | |
| -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 /Users/runner/miniconda3/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" | |
| elif [ ${{ matrix.python-version }} == "3.11" ]; then | |
| export CIBW_BUILD="cp311-macosx_x86_64" | |
| fi | |
| export CIBW_ENVIRONMENT='MACOSX_DEPLOYMENT_TARGET=10.14' | |
| export CIBW_BEFORE_BUILD="python -m pip install colored" | |
| python -m cibuildwheel --output-dir dist | |
| cd dist | |
| cd ../.. | |
| mv core/dist . | |
| - name: Create opengate_core Wheel Windows | |
| if: matrix.os == 'windows-latest' | |
| shell: bash -l {0} | |
| run: | | |
| choco install cmake | |
| cmake --version | |
| conda info | |
| conda list | |
| which python | |
| python --version | |
| export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH" | |
| pip install wheel wget colored | |
| pip install cibuildwheel==2.12.0 | |
| which pip | |
| 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 $GEANT4_VERSION https://github.com/Geant4/geant4.git --depth 1 src | |
| cd bin | |
| cmake -DGEANT4_INSTALL_DATA=ON \ | |
| -DGEANT4_INSTALL_DATADIR=$HOME/software/geant4/data \ | |
| -DGEANT4_BUILD_MULTITHREADED=ON \ | |
| ../src | |
| cmake --build . --config Release | |
| 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 \ | |
| ../src | |
| cmake --build . --config Release | |
| fi | |
| cd $GITHUB_WORKSPACE | |
| source $HOME/software/geant4/bin/geant4make.sh | |
| export CMAKE_PREFIX_PATH=$HOME/software/geant4/bin:$HOME/software/itk/bin/:${CMAKE_PREFIX_PATH} | |
| cd core | |
| if [[ ${{ matrix.python-version }} == "3.8" ]]; then | |
| export CIBW_BUILD="cp38-win_amd64" | |
| elif [[ ${{ matrix.python-version }} == "3.9" ]]; then | |
| export CIBW_BUILD="cp39-win_amd64" | |
| elif [[ ${{ matrix.python-version }} == "3.10" ]]; then | |
| export CIBW_BUILD="cp310-win_amd64" | |
| elif [[ ${{ matrix.python-version }} == "3.11" ]]; then | |
| export CIBW_BUILD="cp311-win_amd64" | |
| fi | |
| find $HOME/software/geant4/bin/ -iname "*.dll" | |
| ls $HOME/software/geant4/bin/BuildProducts/Release/bin | |
| ls $HOME/software/geant4/bin/BuildProducts/Release/lib/ | |
| export CIBW_BEFORE_BUILD="python -m pip install colored" | |
| python -m cibuildwheel --output-dir dist | |
| cd .. | |
| mkdir core/dist2 | |
| pip install pefile machomachomangler | |
| ls core/dist | |
| python $GITHUB_WORKSPACE\\.github\\workflows\\delocateWindows.py core\\dist -w core\\dist2 -d C:\\Users\\runneradmin\\software\\geant4\\bin\\BuildProducts\\Release\\bin | |
| mv core/dist2 dist | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: dist/ | |
| publish_wheel: | |
| runs-on: ubuntu-latest | |
| needs: [build_wheel] | |
| steps: | |
| - name: Checkout github repo | |
| uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: dist-* | |
| merge-multiple: true | |
| 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@release/v1 | |
| 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@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_OPENGATE }} | |
| packages_dir: dist_opengate/ | |
| skip_existing: true | |
| # ssh_session: | |
| # env: | |
| # GEANT4_VERSION: 'v11.2.1' | |
| # ITK_VERSION: 'v5.2.1' | |
| # runs-on: macos-12 | |
| # steps: | |
| # - name: Checkout github repo | |
| # uses: actions/checkout@v4 | |
| # - name: Checkout submodules | |
| # shell: bash -l {0} | |
| # run: | | |
| # export GIT_SSL_NO_VERIFY=1 | |
| # git submodule update --init --recursive | |
| # - name: Set up Python | |
| # uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: 3.9 | |
| # architecture: 'x64' | |
| # - name: Get OS version | |
| # id: get-os-version | |
| # shell: bash -l {0} | |
| # run: | | |
| # varOS=`sw_vers | grep "ProductVersion:"` | |
| # varOS="${varOS#*:}" | |
| # echo "release=${varOS:1}" >> $GITHUB_OUTPUT | |
| # - name: Cache modules | |
| # id: cache_opengate_core_dependencies | |
| # uses: actions/cache@v4 | |
| # with: | |
| # path: ~/software | |
| # key: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build1 | |
| # restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build1 | |
| # - uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # miniconda-version: "latest" | |
| # auto-update-conda: true | |
| # activate-environment: opengate_core | |
| # python-version: 3.9 | |
| # - name: Set up Homebrew | |
| # id: set-up-homebrew | |
| # uses: Homebrew/actions/setup-homebrew@master | |
| # - name: Start SSH session | |
| # uses: luchihoratiu/debug-via-ssh@main | |
| # with: | |
| # NGROK_AUTH_TOKEN: ${{ secrets.NGROK_AUTH_TOKEN }} | |
| # SSH_PASS: ${{ secrets.SSH_PASS }} | |
| test_wheel: | |
| runs-on: ${{ matrix.os }} | |
| needs: [build_wheel] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-12, windows-latest] | |
| python-version: [3.8, 3.9, '3.10', '3.11'] | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: dist-* | |
| merge-multiple: true | |
| path: dist/ | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Run tests | |
| shell: bash {0} | |
| 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" | |
| export PLATFORM="x86_" | |
| pip install torch --extra-index-url https://download.pytorch.org/whl/cpu | |
| elif [[ ${{ matrix.os }} == "macos-12" ]]; then | |
| export OSNAME="macosx" | |
| export PLATFORM="x86_" | |
| which python | |
| python --version | |
| pip install torch | |
| elif [[ ${{ matrix.os }} == "windows-latest" ]]; then | |
| export OSNAME="win" | |
| export PLATFORM="amd" | |
| pip install torch | |
| fi | |
| pip install SimpleITK | |
| pip install gaga_phsp==0.7.1 | |
| pip install dist/opengate_core-*-${PYTHONFOLDER}-${OSNAME}*_${PLATFORM}64.whl | |
| pip install dist/opengate-*.whl | |
| export GIT_SSL_NO_VERIFY=1 | |
| if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then | |
| path=`opengate_library_path.py -p site_packages` | |
| export LD_LIBRARY_PATH="${path}/opengate_core.libs":${LD_LIBRARY_PATH} | |
| path=`opengate_library_path.py -p libG4processes` | |
| export LD_PRELOAD=${path}:${LD_PRELOAD} | |
| path=`opengate_library_path.py -p libG4geometry` | |
| export LD_PRELOAD=${path}:${LD_PRELOAD} | |
| fi | |
| if [[ ${{ matrix.os }} == "windows-latest" ]]; then | |
| path=`opengate_library_path.py -p site_packages` | |
| export LD_LIBRARY_PATH="${path}/opengate_core.libs":${LD_LIBRARY_PATH} | |
| export PATH="${path}\\opengate_core.libs":${PATH} | |
| fi | |
| pip freeze | |
| if [ "${{ github.event_name }}" = "schedule" ]; then | |
| OutputTest=$(opengate_tests) | |
| else | |
| OutputTest=$(opengate_tests -r) | |
| fi | |
| echo "$OutputTest" | |
| OutputTest=$(echo "$OutputTest" | tail -1) | |
| if [[ "$OutputTest" != "True" ]]; then | |
| exit -1 | |
| else | |
| exit 0 | |
| fi |