main.yml

name: CI

on:
  push:
    branches: [ master ]
    tags:
      - '*'
  pull_request:
    branches: [ master ]
  schedule:
    - cron: '0 0 * * 0,3'
  workflow_dispatch:

jobs:
  build_opengate_wheel:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        python-version: [3.9]
    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 ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        architecture: 'x64'
    - name: Create opengate Wheel
      run: |
          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
    - name: Upload wheels
      uses: actions/upload-artifact@v4
      with:
        name: dist-opengate
        path: dist/

  build_opengate_core_wheel:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-13, macos-14, windows-latest]
        python-version: [3.9, '3.10', '3.11', '3.12']
        exclude:
          - os: macos-14
            python-version: 3.9
          - os: macos-14
            python-version: '3.10'

    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 }} == "windows-latest" ]]; then
          set "GIT_SSL_NO_VERIFY=1"
        else
          export GIT_SSL_NO_VERIFY=1
        fi
        git submodule update --init --recursive
    - 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-13" ]] || [[ ${{ matrix.os }} == "macos-14" ]]; then
            varOS=`sw_vers | grep "ProductVersion:"`
            varOS="${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 }}_build2
        restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build2
    - name: Create opengate_core Wheel Linux
      if: matrix.os == 'ubuntu-latest'
      run: |
          if [ ${{ 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"
          elif [ ${{ matrix.python-version }} == "3.12" ]; then
            export PYTHONFOLDER="cp312-cp312"
          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
    - uses: conda-incubator/setup-miniconda@v3
      if: (matrix.os == 'macos-13') || (matrix.os == 'macos-14') || (matrix.os == 'windows-latest')
      with:
          miniconda-version: "latest"
          auto-update-conda: true
          activate-environment: opengate_core
          python-version: ${{ matrix.python-version }}
    - name: Set up Homebrew
      if: (matrix.os == 'macos-13') || (matrix.os == 'macos-14')
      id: set-up-homebrew
      uses: Homebrew/actions/setup-homebrew@master
    - name: Create opengate_core Wheel Mac
      if: (matrix.os == 'macos-13') || (matrix.os == 'macos-14')
      shell: bash -l {0}
      run: |
          brew install python@3.12 || true
          brew link --overwrite python@3.12
          #brew update
          #rm -rf /usr/local/bin/python3.1*-config /usr/local/bin/2to3-3.1* /usr/local/bin/idle3.1* /usr/local/bin/pydoc3.1* /usr/local/bin/python3.1*
          #rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3
          brew install --force --verbose --overwrite \
                       ccache \
                       fftw \
                       libomp \
                       xquartz \
                       xerces-c \
                       wget
          brew uninstall --ignore-dependencies libxext
          brew uninstall --ignore-dependencies libx11
          export LDFLAGS="-L/usr/local/opt/llvm/lib"
          export CPPFLAGS="-I/usr/local/opt/llvm/include -fopenmp"
          conda info
          conda list
          which python
          python --version
          export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH"
          pip install wget colored
          pip install wheel delocate
          if [[ ${{ matrix.os }} == "macos-13" ]]; then          
              conda install conda-forge::qt6-main conda-forge::qt6-3d
          else
              brew install qt
          fi
          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=OFF \
                    -DGEANT4_USE_QT_QT6=ON \
                    -DQT_HOST_PATH=/Users/runner/miniconda3/envs/opengate_core/lib/cmake/Qt6 \
                    -DQT_HOST_PATH_CMAKE_DIR=/Users/runner/miniconda3/envs/opengate_core/lib/cmake/ \
                    -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
          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
          if [[ ${{ matrix.os }} == "macos-13" ]]; the
              cp -r /Users/runner/miniconda3/envs/opengate_core/lib/qt6/plugins/platforms/* opengate_core/plugins/
              cp -r /Users/runner/miniconda3/envs/opengate_core/lib/qt6/plugins/imageformats opengate_core/plugins/
          else
              cp -r /opt/homebrew/share/qt/plugins/platforms/* opengate_core/plugins/
              cp -r /opt/homebrew/share/qt/plugins/imageformats/* opengate_core/plugins/
          fi
          python3 setup.py sdist bdist_wheel
          ls dist
          export DYLD_LIBRARY_PATH=$HOME/software/geant4/bin/BuildProducts/lib:/Users/runner/miniconda3/envs/opengate_core/lib/qt6/plugins/platforms:/opt/X11/lib/:$DYLD_LIBRARY_PATH:/Users/runner/miniconda3/envs/opengate_core/lib
          delocate-listdeps --all dist/*.whl
          delocate-wheel -w fixed_wheels -v dist/*.whl
          rm -rf dist
          ls fixed_wheels
          delocate-listdeps --all fixed_wheels/*.whl
          mv fixed_wheels dist
          cd dist
          if [[ ${{ matrix.os }} == "macos-13" ]]; then
              find . -name '*whl' -exec bash -c ' mv $0 ${0/macosx_13_0/macosx_10_9}' {} \;
          cd ../..
          mv core/dist .
    - name: Create opengate_core Wheel Windows
      if: matrix.os == 'windows-latest'
      shell: bash -l {0}
      run: |
          choco install cmake
          cmake --version
          conda info
          conda list
          which python
          python --version
          export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH"
          pip install wheel wget colored
          pip install cibuildwheel==2.21.1
          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 }} == "3.9" ]]; 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"
          elif [[ ${{ matrix.python-version }} == "3.12" ]]; then
            export CIBW_BUILD="cp312-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 }}-opengate-core
        path: dist/

  build_opengate_core_novis_wheel:
    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/')
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        python-version: [3.9, '3.10', '3.11', '3.12']

    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: |
        export GIT_SSL_NO_VERIFY=1
        git submodule update --init --recursive
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        architecture: 'x64'
    - name: Get OS version
      id: get-os-version
      shell: bash -l {0}
      run: |
        varOS=`cat /etc/os-release | grep "VERSION=" | grep -oP '(?<=\").*?(?=\")'`
        varOS=($varOS)
        echo "release=${varOS[0]}" >> $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 }}_build2
        restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build2
    - name: Create opengate_core_novis Wheel Linux
      run: |
          if [ ${{ 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"
          elif [ ${{ matrix.python-version }} == "3.12" ]; then
            export PYTHONFOLDER="cp312-cp312"
          fi
          mkdir -p $HOME/software
          docker run --rm -e "PYTHONFOLDER=${PYTHONFOLDER}" -v $GITHUB_WORKSPACE:/home tbaudier/opengate_core:${{ env.GEANT4_VERSION }}_novis /home/.github/workflows/createWheelLinux_novis.sh
          ls wheelhouse
          rm -rf dist
          mv wheelhouse dist
          sudo chown -R runner:docker dist
    - name: Upload wheels
      uses: actions/upload-artifact@v4
      with:
        name: dist-${{ matrix.os }}-${{ matrix.python-version }}-opengate-core-novis
        path: dist/

  publish_wheel:
    runs-on: ubuntu-latest
    needs: [build_opengate_wheel, build_opengate_core_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 dist_opengate_core_novis
          mv dist/opengate_core_novis-* dist_opengate_core_novis/ || true
          mv dist/opengate_core-* dist_opengate_core/
          mv dist/opengate-* dist_opengate/
    - name: Publish to PyPI opengate_core_novis
      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_NOVIS }}
        packages_dir: dist_opengate_core_novis/
        skip_existing: true
    - 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-13
#    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 }}_build2
#        restore-keys: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build2
#    - 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_opengate_wheel, build_opengate_core_wheel]
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-13, windows-latest]
        python-version: [3.9, '3.10', '3.11', '3.12']
    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 }} == "3.9" ]]; 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"
          elif [[ ${{ matrix.python-version }} == "3.12" ]]; then
            export PYTHONFOLDER="cp312-cp312"
          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-13" ]]; then
            export OSNAME="macosx"
            export PLATFORM="x86_"
            which python
            python --version
            pip install torch
          elif [[ ${{ matrix.os }} == "windows-latest" ]]; then
            export OSNAME="win"
            export PLATFORM="amd"
            pip install torch
          fi
          pip install SimpleITK
          pip install gaga_phsp==0.7.4
          pip install spekpy
          pip install dist/opengate_core-*-${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}
          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":${PATH}
          fi
          dashboard_path=`opengate_library_path.py -p tests`
          pip freeze
          if [ "${{ github.event_name }}" = "schedule" ]; then
              OutputTest=$(opengate_tests)
          else
              OutputTest=$(opengate_tests -r)
          fi
          echo "$OutputTest"
          ls $dashboard_path/../output_dashboard/
          cp -r $dashboard_path/../output_dashboard .
          OutputTest=$(echo "$OutputTest" | tail -1)
          if [[ "$OutputTest" != "True" ]]; then
              exit -1
          else
              exit 0
          fi
    - name: Upload results
      uses: actions/upload-artifact@v4
      if: always()
      with:
        name: results_json-${{ matrix.os }}-${{ matrix.python-version }}
        path: output_dashboard/dashboard_output*.json

  publish_test:
    runs-on: ubuntu-latest
    if: ${{ (always()) && (github.ref == 'refs/heads/master') }}
    needs: [test_wheel]
    steps:
    - name: Checkout github repo
      uses: actions/checkout@v4
    - uses: actions/download-artifact@v4
      with:
        pattern: results_json-*
        merge-multiple: true
        path: ./
    - uses: conda-incubator/setup-miniconda@v3
      with:
          miniconda-version: "latest"
          auto-update-conda: true
          activate-environment: vega-altair
          python-version: '3.10'
    - name: Merge the results
      shell: bash -el {0}
      run: |
          git clone https://github.com/OpenGATE/opengate_tests_results.git
          cd opengate_tests_results
          echo $pwd
          ls ..
          cp ../dashboard_output_*.json .
          conda install -c conda-forge altair-all
          pip install pandas numpy
          python compile_opengate_tests_results.py
    - name: Pushes to another repository
      continue-on-error: true
      uses: cpina/github-action-push-to-another-repository@main
      env:
          API_TOKEN_GITHUB: ${{ secrets.PUSH_OPENGATE_TESTS_RESULTS }}
      with:
          source-directory: 'opengate_tests_results'
          destination-github-username: 'OpenGATE'
          destination-repository-name: 'opengate_tests_results'
          user-email: tbaudier@creatis.insa-lyon.fr
          target-branch: master