Rebase to current master

Author: alexvergaragil

.github/workflows/actions_build/action.yml

@@ -45,7 +45,7 @@ runs:
         fi
     - name: Cache modules
       id: cache_opengate_core_dependencies
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       with:
         path: ~/software
         key: ${{ runner.os }}-${{ steps.get-os-version.outputs.release }}_geant4_${{ env.GEANT4_VERSION }}_itk_${{ env.ITK_VERSION }}_build
@@ -66,6 +66,7 @@ runs:
       env:
         MATRIX_OS: ${{ inputs.os }}
         MATRIX_PYTHON_VERSION: ${{ inputs.python-version }}
+        MATRIX_CACHE: ${{ steps.cache_opengate_core_dependencies.outputs.cache-hit }}
       shell: bash -l {0}
       run: |
           export > $GITHUB_WORKSPACE/env_dump.txt
@@ -85,6 +86,7 @@ runs:
       env:
         MATRIX_CACHE: ${{ steps.cache_opengate_core_dependencies.outputs.cache-hit }}
         MATRIX_PYTHON_VERSION: ${{ inputs.python-version }}
+        MATRIX_OS: ${{ inputs.os }}
       shell: bash -l {0}
       run: |
           export > $GITHUB_WORKSPACE\\env_dump.txt

.github/workflows/actions_build/ci_build_wheel_macos.sh

@@ -2,29 +2,21 @@
 set -e
 
 source $GITHUB_WORKSPACE/env_dump.txt
-brew install python@${MATRIX_PYTHON_VERSION} || true
-brew link --overwrite python@${MATRIX_PYTHON_VERSION}
-#brew update
-#rm -rf /usr/local/bin/python3.1*-config /usr/local/bin/2to3-3.1* /usr/local/bin/idle3.1* /usr/local/bin/pydoc3.1* /usr/local/bin/python3.1*
-#rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3
 brew install --force --verbose --overwrite \
              ccache \
              fftw \
              libomp \
              xquartz \
-             xerces-c \
-             wget  || true
+             xerces-c || true
 brew uninstall --ignore-dependencies libxext
 brew uninstall --ignore-dependencies libx11
 export LDFLAGS="-L/usr/local/opt/llvm/lib"
 export CPPFLAGS="-I/usr/local/opt/llvm/include -fopenmp"
 conda info
 conda list
-which python
-python --version
 export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH"
 pip install wget colored
-pip install wheel delocate
+pip install cibuildwheel[uv]==3.4.0
 if [[ ${MATRIX_OS} == "macos-15-intel" ]]; then
     conda install conda-forge::qt6-main conda-forge::qt6-3d
 else
@@ -75,20 +67,22 @@ 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 CIBW_BUILD_FRONTEND="build[uv]"
+export CIBW_PLATFORM="macos"
+export CIBW_SKIP="*t*"
+export MACOSX_DEPLOYMENT_TARGET=15.0
+export CIBW_BEFORE_BUILD="uv pip install colored"
+
 if [[ ${MATRIX_OS} == "macos-15-intel" ]]; then
     export DYLD_LIBRARY_PATH=$HOME/software/geant4/bin/BuildProducts/lib:/Users/runner/miniconda3/envs/opengate_core/lib/qt6/plugins/platforms:/opt/X11/lib/:$DYLD_LIBRARY_PATH:/Users/runner/miniconda3/envs/opengate_core/lib
+    export CIBW_ARCHS_MACOS="x86_64"
 else
     export DYLD_LIBRARY_PATH=$HOME/software/geant4/bin/BuildProducts/lib:/opt/homebrew/share/qt/plugins/platforms/:/opt/X11/lib/:$DYLD_LIBRARY_PATH:/opt/homebrew/lib
+    export CIBW_ARCHS_MACOS="arm64"
     python -c "import os,delocate; print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()" | xargs -I{} sed -i."" "s/first, /input.pop('i386',None); first, /g" {}
 fi
-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
+
+python -m cibuildwheel --output-dir dist
 cd dist
 if [[ ${MATRIX_OS} == "macos-15-intel" ]]; then
     find . -name '*whl' -exec bash -c ' mv $0 ${0/macosx_15_0/macosx_10_9}' {} \;

.github/workflows/actions_build/ci_build_wheel_ubuntu.sh

@@ -2,23 +2,43 @@
 set -e
 
 source $GITHUB_WORKSPACE/env_dump.txt
-if [ ${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"
-elif [ ${MATRIX_PYTHON_VERSION} == "3.13" ]; then
-  export PYTHONFOLDER="cp313-cp313"
-elif [ ${MATRIX_PYTHON_VERSION} == "3.14" ]; then
-  export PYTHONFOLDER="cp314-cp314"
-fi
-mkdir -p $HOME/software
+
+# install cibuildwheel
+pip install cibuildwheel[uv]==3.4.0
+pip install wget colored setuptools
+
+# Setup the environment for the build
 if [ ${MATRIX_OS} == "ubuntu-24.04-arm" ]; then
   export ARMDOCKER="_arm64"
+  export CIBW_ARCHS="aarch64"
+  export CIBW_MANYLINUX_AARCH64_IMAGE=tbaudier/opengate_core:${GEANT4_VERSION}$ARMDOCKER
+else
+  export CIBW_ARCHS="x86_64"
+  export CIBW_MANYLINUX_X86_64_IMAGE=tbaudier/opengate_core:${GEANT4_VERSION}
 fi
-docker run --rm -e "PYTHONFOLDER=${PYTHONFOLDER}" -v $GITHUB_WORKSPACE:/home tbaudier/opengate_core:${GEANT4_VERSION}$ARMDOCKER /home/.github/workflows/createWheelLinux.sh
-ls wheelhouse
-rm -rf dist
-mv wheelhouse dist
-sudo chown -R runner:docker dist
+export CIBW_PLATFORM="linux"
+export CIBW_BUILD_FRONTEND="build[uv]"
+export CIBW_SKIP="*-musllinux_* *t*"
+export CIBW_BEFORE_BUILD='
+pip install colored &&
+mkdir -p opengate_core/plugins &&
+export QT_PLUGIN_DIR=$(qtpaths6 --plugin-dir) &&
+cp -r -n $QT_PLUGIN_DIR/platforms/* opengate_core/plugins/ &&
+cp -r -n $QT_PLUGIN_DIR/imageformats opengate_core/plugins/ &&
+source /software/geant4/bin/geant4make.sh &&
+. /opt/rh/gcc-toolset-14/enable
+'
+
+# expose external libraries to build environment
+export CIBW_ENVIRONMENT='
+CMAKE_PREFIX_PATH=/software/geant4/bin:/software/itk/bin/
+Geant4_DIR=/software/geant4/lib/cmake/Geant4
+ITK_DIR=/software/itk/lib/cmake/ITK
+LD_LIBRARY_PATH=/software/geant4/lib:/software/itk/lib
+'
+
+# Run the build in custom docker
+cd core
+python -m cibuildwheel --output-dir dist
+mkdir -p $GITHUB_WORKSPACE/dist
+mv dist/*.whl $GITHUB_WORKSPACE/dist/

.github/workflows/actions_build/ci_build_wheel_windows.sh

@@ -11,9 +11,9 @@ conda list
 which python
 python --version
 export PATH="/usr/local/miniconda/envs/opengate_core/bin/:$PATH"
-pip install wheel wget colored
+pip install wget colored delvewheel
 
-pip install cibuildwheel==3.4.0
+pip install cibuildwheel[uv]==3.4.0
 
 # For windows 2025, Need to add the certifi CA bundle to avoid SSL errors when downloading dependencies during the build. This is a workaround for cibuildwheel which does not handle this properly on Windows.
 python - << 'EOF'
@@ -54,25 +54,27 @@ 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} == "3.10" ]]; 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"
-elif [[ ${MATRIX_PYTHON_VERSION} == "3.13" ]]; then
-  export CIBW_BUILD="cp313-win_amd64"
-elif [[ ${MATRIX_PYTHON_VERSION} == "3.14" ]]; then
-  export CIBW_BUILD="cp314-win_amd64"
+echo ${MATRIX_OS}
+if [[ ${MATRIX_OS} == "windows-11-arm" ]]; then
+    export CIBW_ARCHS="ARM64"
+else
+    export CIBW_ARCHS="AMD64"
 fi
+export CIBW_BUILD_FRONTEND="build[uv]"
+export CIBW_SKIP="*t*"
+export CIBW_PLATFORM="windows"
 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"
+
+# use delvewheel on windows
+export CIBW_BEFORE_BUILD_WINDOWS="uv pip install colored"
+export CIBW_REPAIR_WHEEL_COMMAND_WINDOWS=''
 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
+delvewheel repair -w core/dist2 core/dist/*.whl --add-path $HOME/software/geant4/bin/BuildProducts/Release/bin -vv
+
+ls core/dist2
 mv core/dist2 dist