main.yml

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, windows-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
      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-latest" ]]; 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@v4
      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 [[ ${{ matrix.os }} == "macos-latest" ]]; then
            varOS=`sw_vers | grep "ProductVersion:"`
            varOS="${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@v3
      with:
        path: ~/software
        key: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build5
        restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build5
    - 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') || (matrix.os == 'windows-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 [ ${{ matrix.python-version }} == "3.10" ]; then
            export CIBW_BUILD="cp310-macosx_x86_64"
          fi
          export CIBW_BEFORE_BUILD="python -m pip install colored"
          python -m cibuildwheel --output-dir dist
          cd dist
          cd ../..
          mv core/dist .
    - name: Create opengate_core Wheel Windows
      if: matrix.os == 'windows-latest'
      shell: bash -l {0}
      run: |
          choco install cmake
          cmake --version
          conda info
          conda list
          which python
          python --version
          export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$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="cp310-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 pefile machomachomangler"
          #export CIBW_REPAIR_WHEEL_COMMAND_WINDOWS="delvewheel repair -vv --add-path $HOME/software/geant4/bin/BuildProducts/Release/lib/ -w {dest_dir} {wheel}"
          #export CIBW_REPAIR_WHEEL_COMMAND_WINDOWS="delvewheel show -vv --add-path $HOME/software/geant4/bin/BuildProducts/Release/bin/ {wheel}"
          #export CIBW_REPAIR_WHEEL_COMMAND_WINDOWS="python $GITHUB_WORKSPACE\\.github\\workflows\\delocateWindows.py {wheel} -w {dest_dir} -d C:\Users\runneradmin\software\geant4\bin\BuildProducts\Release\bin"
          python -m cibuildwheel --output-dir dist
          cd ..
          mkdir core/dist2
          #mv core/dist .
          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@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

  ssh_session:
    runs-on: windows-latest
    needs: [build_wheel]
    steps:
    - uses: actions/download-artifact@v3
      with:
        name: dist
        path: dist/
    - name: Set up Python 3.9
      uses: actions/setup-python@v4
      with:
       python-version: 3.9
       architecture: 'x64'
    - 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, windows-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
      shell: bash -l {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-latest" ]]; then
            export OSNAME="macosx"
            export PLATFORM="x86_"
            pip install torch
          elif [[ ${{ matrix.os }} == "windows-latest" ]]; then
            export OSNAME="win"
            export PLATFORM="amd"
            pip install torch
          fi
          pip install gaga_phsp
          pip install garf
          pip install dist/opengate_core-*-${PYTHONFOLDER}-${OSNAME}*_${PLATFORM}64.whl
          pip install dist/opengate-*.whl
          export GIT_SSL_NO_VERIFY=1
          if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then
              path=`opengate_tests_utils -p site_packages`
              export LD_LIBRARY_PATH="${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
          if [[ ${{ matrix.os }} == "windows-latest" ]]; then
              pip install msvc-runtime wget
              path=`opengate_tests_utils -p site_packages`
              export LD_LIBRARY_PATH="${path}/opengate_core.libs":${LD_LIBRARY_PATH}
              export PATH="${path}\\opengate_core.libs":${PATH}
              #path=`opengate_tests_utils -p libG4processes`
              #export LD_PRELOAD=${path}:${LD_PRELOAD}
              #path=`opengate_tests_utils -p libG4geometry`
              #export LD_PRELOAD=${path}:${LD_PRELOAD}
          fi
          pip freeze
          #dumpbin C:\hostedtoolcache\windows\Python\3.9.13\x64\Scripts\opengate_tests
          OutputTest=$(opengate_tests)
          echo "$OutputTest"
          OutputTest=$(echo "$OutputTest" | tail -1)
          if [[ "$OutputTest" != "True" ]]; then
              exit -1
          else
              exit 0
          fi