CI #2109
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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 |