geant4-python-application 0.1.0__tar.gz

geant4_python_application-0.1.0/.clang-format

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geant4_python_application-0.1.0/.cmake-format.yaml

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+# https://cmake-format.readthedocs.io/en/latest/configuration.html
+
+format:
+  tab_size: 4
+  separate_ctrl_name_with_space: true
+  separate_fn_name_with_space: false

geant4_python_application-0.1.0/.dockerignore

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+venv
+build
+*-build-*
+*_cache
+.github
+tests

geant4_python_application-0.1.0/.github/CODEOWNERS

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+* @lobis

geant4_python_application-0.1.0/.github/dependabot.yaml

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+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly

geant4_python_application-0.1.0/.github/workflows/build-test.yaml

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+name: Build and Test
+
+on:
+  schedule:
+    - cron: 0 */24 * * *
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+env:
+  GEANT4_VERSION: 11.2.2
+  XERCES_VERSION: 3.2.5
+  CPP_STANDARD: 17
+  Geant4_DIR: ${{ github.workspace }}/geant4
+
+jobs:
+  install-with-geant4-from-conda:
+    name: Install dependencies with conda
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest] # Geant4 is not available on conda for windows TODO: update this when it is
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: 3.12
+
+      - name: Install Geant4 and cmake using conda
+        run: |
+          conda install -c conda-forge cmake ninja geant4=${{ env.GEANT4_VERSION }}
+
+      - name: Install additional dependencies (Ubuntu)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          conda install -c conda-forge gxx_linux-64
+
+      - name: Install additional dependencies (MacOS)
+        if: matrix.os == 'macos-latest'
+        run: |
+          conda install -c conda-forge clang_osx-64
+
+      - name: Print versions
+        run: |
+          conda --version
+          cmake --version
+
+          echo "Geant4: ${{ env.GEANT4_VERSION }}"
+
+          geant4-config --version
+          geant4-config --check-datasets
+
+      - name: Install datasets if missing # Shouldn't they be available after the conda install?
+        run: |
+          geant4-config --install-datasets
+          geant4-config --check-datasets
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: pip install the package from source
+        run: |
+          python -m pip install .[test]
+          python -c "import geant4_python_application; print(geant4_python_application.version)"
+
+      - name: Check datasets are accessible # Datasets should have been installed by the conda package, and should be accessible
+        run: |
+          python -c "import geant4_python_application as g4; g4.files.datasets.check_datasets(throw=True)"
+
+      - name: Run tests
+        run: |
+          python -m pytest -vv --reruns 3 --reruns-delay 30 --only-rerun "(?i)http|timeout|connection|socket|resolve"
+
+  build-geant4:
+    name: Build Geant4 on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - name: Setup CMake
+        uses: lukka/get-cmake@v3.30.3
+
+      - name: Cache Xerces-C Installation
+        id: cache-xerces
+        uses: actions/cache@v4
+        with:
+          path: ${{ github.workspace }}/xerces
+          key: xerces-v${{ env.XERCES_VERSION }}-cpp${{ env.CPP_STANDARD }}
+
+      - name: Build and Install Xerces-C
+        if: steps.cache-xerces.outputs.cache-hit != 'true'
+        run: |
+          git clone https://github.com/apache/xerces-c.git xerces-source
+          git -C xerces-source checkout tags/v${{ env.XERCES_VERSION }}
+          cmake -B xerces-build -S xerces-source -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${{ github.workspace }}/xerces -DCMAKE_CXX_STANDARD=${{ env.CPP_STANDARD }} -DBUILD_SHARED_LIBS=OFF ${{ matrix.os == 'windows-latest' && '-DCMAKE_MSVC_RUNTIME_LIBRARY=MultiThreaded -DCMAKE_CXX_FLAGS_RELEASE="/MT"' || '-G Ninja -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_C_FLAGS=-fPIC -Dnetwork-accessor=socket -Dtranscoder=iconv' }}
+          cmake --build xerces-build --parallel $(nproc) --config Release --target install
+
+      - name: Cache Geant4 Installation
+        id: cache-geant4
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.Geant4_DIR }}
+          key: geant4-v${{ env.GEANT4_VERSION }}-cpp${{ env.CPP_STANDARD }}
+
+      - name: Build and Install Geant4 (without datasets)
+        if: steps.cache-geant4.outputs.cache-hit != 'true'
+        run: |
+          git clone https://github.com/Geant4/geant4.git ${{ github.workspace }}/geant4-source --depth 1 --branch v${{ env.GEANT4_VERSION }}
+          cmake -B geant4-build -S geant4-source -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${{ env.Geant4_DIR }} -DXERCESC_ROOT_DIR=${{ github.workspace }}/xerces -DCMAKE_CXX_STANDARD=${{ env.CPP_STANDARD }} -DGEANT4_USE_GDML=ON -DGEANT4_INSTALL_EXAMPLES=OFF -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_TLS_MODEL=global-dynamic -DBUILD_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF ${{ matrix.os == 'windows-latest' && '-DCMAKE_MSVC_RUNTIME_LIBRARY=MultiThreaded -DCMAKE_CXX_FLAGS_RELEASE="/MT"' || '-G Ninja -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_C_FLAGS=-fPIC -DGEANT4_USE_SYSTEM_EXPAT=OFF' }}
+          cmake --build geant4-build --parallel $(nproc) --config Release --target install
+
+  install-geant4-datasets:
+    name: Download Geant4 datasets for ${{ matrix.os }}
+    needs: [build-geant4]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - name: Cache Geant4 Installation
+        id: cache-geant4
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.Geant4_DIR }}
+          key: geant4-v${{ env.GEANT4_VERSION }}-cpp${{ env.CPP_STANDARD }}
+          fail-on-cache-miss: true
+
+      - name: Cache Geant4 Datasets
+        id: cache-geant4-data
+        uses: actions/cache@v4
+        with:
+          path: ${{ github.workspace }}/geant4-data
+          key: geant4-${{ env.GEANT4_VERSION }}-data
+          enableCrossOsArchive: true
+          lookup-only: true
+
+      - name: Move Geant4 datasets (Ubuntu/MacOS)
+        if:
+          steps.cache-geant4-data.outputs.cache-hit != 'true' && matrix.os !=
+          'windows-latest'
+        shell: bash
+        run: |
+          bash ${{ env.Geant4_DIR }}/bin/geant4-config --install-datasets
+          bash ${{ env.Geant4_DIR }}/bin/geant4-config --check-datasets
+          mv ${{ env.Geant4_DIR }}/share/Geant4/data ${{ github.workspace }}/geant4-data
+
+      - name: Move Geant4 datasets (Windows)
+        if:
+          steps.cache-geant4-data.outputs.cache-hit != 'true' && matrix.os ==
+          'windows-latest'
+        shell: powershell
+        run: |
+          Get-ChildItem -Path  ${{ env.Geant4_DIR }}\bin
+          cmd /c  ${{ env.Geant4_DIR }}\bin\geant4-config.cmd --install-datasets
+          cmd /c  ${{ env.Geant4_DIR }}\bin\geant4-config.cmd --check-datasets
+          Move-Item ${{ env.Geant4_DIR }}\share\Geant4\data ${{ github.workspace }}\geant4-data
+
+  build-test:
+    name:
+      Build and Test for ${{ matrix.os }} (Python ${{ matrix.python-version }})
+    needs: [install-geant4-datasets]
+    timeout-minutes: 30
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup CMake
+        uses: lukka/get-cmake@v3.30.3
+
+      - name: Setup Windows environment variables
+        if: matrix.os == 'windows-latest'
+        shell: bash
+        run: |
+          echo "CMAKE_ARGS=-DCMAKE_MSVC_RUNTIME_LIBRARY=MultiThreaded" >> $GITHUB_ENV
+
+      - name: Cache Xerces-C Installation
+        id: cache-xerces
+        uses: actions/cache@v4
+        with:
+          path: ${{ github.workspace }}/xerces
+          key: xerces-v${{ env.XERCES_VERSION }}-cpp${{ env.CPP_STANDARD }}
+          fail-on-cache-miss: true
+
+      - name: Cache Geant4 Installation
+        id: cache-geant4
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.Geant4_DIR }}
+          key: geant4-v${{ env.GEANT4_VERSION }}-cpp${{ env.CPP_STANDARD }}
+          fail-on-cache-miss: true
+
+      - name: pip install the package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[test]
+          git tag
+          python -c "import geant4_python_application; print(geant4_python_application.version)"
+
+      # test ability to download datasets in one job and use the cache in the others
+      - name: Cache Geant4 Datasets
+        if: matrix.python-version != '3.11'
+        id: cache-geant4-data
+        uses: actions/cache@v4
+        with:
+          path: ${{ github.workspace }}/geant4-data
+          key: geant4-${{ env.GEANT4_VERSION }}-data
+          fail-on-cache-miss: true
+          enableCrossOsArchive: true
+
+      - name: Move Geant4 datasets (Ubuntu/MacOS)
+        if: matrix.python-version != '3.11' && matrix.os != 'windows-latest'
+        run: |
+          GEANT4_DATA_DIR=$(python -c "import geant4_python_application; print(geant4_python_application.data_directory())")
+          mkdir -p ${{ github.workspace }}/geant4-data "$GEANT4_DATA_DIR"
+          mv ${{ github.workspace }}/geant4-data/* "$GEANT4_DATA_DIR"
+
+      # TODO: unify this with the above
+      - name: Move Geant4 datasets (Windows)
+        if: matrix.python-version != '3.11' && matrix.os == 'windows-latest'
+        shell: powershell
+        run: |
+          $env:GEANT4_DATA_DIR = python -c "import geant4_python_application; print(geant4_python_application.data_directory())"
+          New-Item -ItemType Directory -Path "${{ github.workspace }}\geant4-data" -Force
+          New-Item -ItemType Directory -Path $env:GEANT4_DATA_DIR -Force
+          Move-Item "${{ github.workspace }}\geant4-data\*" $env:GEANT4_DATA_DIR -Force
+
+      - name: Install datasets
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          retry_wait_seconds: 60
+          max_attempts: 5
+          command: |
+            python -c "import geant4_python_application as g4; g4.install_datasets()"
+            # Check that the datasets are installed correctly
+            python -c "import geant4_python_application as g4; g4.files.datasets.check_datasets(throw=True)"
+
+      - name: Run tests
+        run: |
+          python -m pytest -vv --reruns 3 --reruns-delay 30 --only-rerun "(?i)http|timeout|connection|socket|resolve"
+
+      - name: Run example notebooks
+        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
+        run: |
+          python -m pip install jupyter nbconvert matplotlib
+          for notebook in $(find examples -name '*.ipynb'); do
+            jupyter nbconvert --to notebook --execute --inplace $notebook
+          done