muGrid 0.0.0__tar.gz

mugrid-0.0.0/.clang-format

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+AccessModifierOffset: -1
+IndentWidth: 4
+UseTab: Never
+SpacesBeforeTrailingComments: 2
+NamespaceIndentation: All
+SortIncludes: false
+SortUsingDeclarations: false
+PointerAlignment: Middle
+AlwaysBreakTemplateDeclarations: true

mugrid-0.0.0/.gitattributes

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+# Tags in this file will be replaced during git archive. git archive is used
+# by meson to create source packages.
+discover_version.py export-subst

mugrid-0.0.0/.github/install_netcdf4.sh

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+#!/bin/bash
+set -e
+
+echo "uname -a is:"
+uname -a
+echo "============"
+
+echo "Environment variables are:"
+printenv
+echo "=========================="
+
+# Determine install prefix based on platform
+OS_TYPE=$(uname -s)
+echo "Detected OS: ${OS_TYPE}"
+
+if [ -z "$INSTALL_PREFIX" ]; then
+    if [ "$OS_TYPE" = "Darwin" ]; then
+        # macOS - use Homebrew prefix
+        brew install pkg-config cmake
+        INSTALL_PREFIX=$(brew --prefix)
+    else
+        # Linux - use /usr/local
+        INSTALL_PREFIX=/usr/local
+    fi
+fi
+
+export PATH=${INSTALL_PREFIX}/bin:${PATH}
+export PKG_CONFIG_PATH=${INSTALL_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}
+
+echo "Installing into prefix ${INSTALL_PREFIX}..."
+echo "PATH is ${PATH}"
+echo "PKG_CONFIG_PATH is ${PKG_CONFIG_PATH}"
+
+# Build libxml2 from source (required for NetCDF on some platforms)
+XML2_VERSION="2.15.1"
+echo "Installing libxml2-${XML2_VERSION}"
+curl -L https://download.gnome.org/sources/libxml2/2.15/libxml2-${XML2_VERSION}.tar.xz | tar -Jx
+mkdir -p build-libxml2
+cd build-libxml2
+cmake \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+    -DBUILD_SHARED_LIBS=OFF \
+    -DLIBXML2_WITH_PYTHON=OFF \
+    -DLIBXML2_WITH_TESTS=OFF \
+    -DLIBXML2_WITH_PROGRAMS=OFF \
+    ../libxml2-${XML2_VERSION}
+cmake --build . --parallel
+cmake --install .
+cd ..
+rm -rf build-libxml2 libxml2-${XML2_VERSION}
+
+# Build NetCDF from source using CMake
+NETCDF_VERSION="4.9.3"
+echo "Installing netcdf-c-${NETCDF_VERSION}"
+curl -L https://github.com/Unidata/netcdf-c/archive/refs/tags/v${NETCDF_VERSION}.tar.gz | tar -zx
+mkdir -p build-netcdf
+cd build-netcdf
+cmake \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
+    -DCMAKE_VERBOSE_MAKEFILE=ON \
+    -DBUILD_SHARED_LIBS=OFF \
+    -DBUILD_TESTING=OFF \
+    -DBUILD_TESTSETS=OFF \
+    -DNETCDF_BUILD_UTILITIES=OFF \
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+    -DNETCDF_ENABLE_CDF5=ON \
+    -DNETCDF_ENABLE_DAP=OFF \
+    -DNETCDF_ENABLE_DAP2=OFF \
+    -DNETCDF_ENABLE_DAP4=OFF \
+    -DNETCDF_ENABLE_HDF5=OFF \
+    -DNETCDF_ENABLE_PLUGINS=OFF \
+    ../netcdf-c-${NETCDF_VERSION}
+cmake --build . --parallel
+cmake --install .
+cd ..
+rm -rf build-netcdf netcdf-c-${NETCDF_VERSION}
+
+echo "NetCDF installation complete!"
+echo "Checking pkg-config:"
+pkg-config --modversion netcdf || echo "Warning: pkg-config netcdf not found"
+pkg-config --libs netcdf || echo "Warning: pkg-config netcdf libs not found"

mugrid-0.0.0/.github/workflows/documentation.yml

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+
+concurrency:
+  group: documentation-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y \
+            python3-dev \
+            python3-pip \
+            python3-venv \
+            doxygen \
+            meson \
+            ninja-build
+          python3 -m venv ../venv
+          source ../venv/bin/activate
+          pip install -r doc/requirements.txt
+
+      - name: Build documentation
+        run: |
+          source ../venv/bin/activate
+          cd doc
+          doxygen
+          make html
+          cd ..
+
+      - name: Commit documentation changes
+        run: |
+          git clone https://github.com/muSpectre/muGrid.git --branch gh-pages --single-branch gh-pages
+          cp -r doc/build/html/* gh-pages/
+          cd gh-pages
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add .
+          git commit -m "Update documentation" -a || true
+          # The above command will fail if no changes were present, so we ignore
+          # that.
+
+      - name: Push documentation changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}

mugrid-0.0.0/.github/workflows/publish.yml

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+name: Publish
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Installing Python
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y \
+            python3-dev \
+            python3-pip \
+            python3-venv \
+            meson \
+            ninja-build
+          python3 -m venv ../venv
+          source ../venv/bin/activate
+          pip install build
+
+      - name: Build source package
+        run: |
+          source ../venv/bin/activate
+          python3 -m build . -s
+
+      - name: Test installation of source package
+        run: |
+          source ../venv/bin/activate
+          pip install dist/*.tar.gz
+
+      - name: Publish package on PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+

mugrid-0.0.0/.github/workflows/tests.yml

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+name: Tests
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+  schedule:
+    - cron: "0 2 * * 5"
+jobs:
+  tests:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 45
+
+    strategy:
+      matrix:
+        mpi: [ 'no', 'yes' ]
+        compiler: [ 'gcc', 'clang' ]
+        python-version: [ '3.10', '3.14' ]
+        numpy-version: [ '>=2.1.0' ]
+        mpi4py-version: [ '==4.0.3' ]
+        exclude:
+          - mpi: 'yes'
+            compiler: 'clang'
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -qy
+          if [ "${{ matrix.compiler }}" == "clang" ]; then
+            sudo apt-get install -y clang
+          fi
+          python3 -m venv venv
+          source venv/bin/activate
+          python3 -m pip install --upgrade pip
+          # Install numpy
+          pip install -v "numpy${{ matrix.numpy-version }}"
+          if [ "${{ matrix.mpi }}" == "yes" ]; then
+            sudo apt-get install -y \
+              cmake \
+              ninja-build \
+              libboost-test-dev \
+              openmpi-bin \
+              libopenmpi-dev \
+              libpnetcdf-dev \
+              libnetcdf-dev
+            # Install mpi4py
+            echo "Installing mpi4py${{ matrix.mpi4py-version }}"
+            CC=mpicc python3 -m pip install -v \
+              --no-binary mpi4py \
+              "mpi4py${{ matrix.mpi4py-version }}"
+          else
+            sudo apt-get install -y \
+              cmake \
+              ninja-build \
+              libboost-test-dev \
+              libnetcdf-dev
+          fi
+          python3 -m pip install build pytest numpy NuMPI[test] netCDF4
+          python3 -m pip list
+
+      - name: Compile with CMake
+        run: |
+          if [ "${{ matrix.compiler }}" == "clang" ]; then
+            export CC=clang
+            export CXX=clang++
+          fi
+          source venv/bin/activate
+          # Explicitly tell CMake to use the venv Python so pytest is found
+          cmake -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$(which python3)
+          cd build
+          cmake --build .
+
+      - name: Run tests
+        run: |
+          source venv/bin/activate
+          cd build
+          ctest --output-on-failure
+
+      - name: Test installation of Python extension module
+        run: |
+          source venv/bin/activate
+          python3 -m pip install .
+
+  # CUDA compile-only test (no GPU required)
+  cuda-compile:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Install CUDA Toolkit
+        uses: Jimver/cuda-toolkit@v0.2.29
+        id: cuda-toolkit
+        with:
+          cuda: '12.6.3'
+          method: 'network'
+          sub-packages: '["nvcc", "cudart-dev"]'
+          non-cuda-sub-packages: '["libcufft-dev"]'
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y \
+            cmake \
+            ninja-build \
+            libboost-test-dev
+
+      - name: Compile with CUDA enabled
+        run: |
+          echo "CUDA Toolkit installed at: ${{ steps.cuda-toolkit.outputs.CUDA_PATH }}"
+          nvcc --version
+          cmake -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DMUGRID_ENABLE_CUDA=ON \
+            -DMUGRID_ENABLE_PYTHON=OFF \
+            -DMUGRID_ENABLE_MPI=OFF \
+            -DMUGRID_ENABLE_NETCDF=OFF \
+            -DMUGRID_ENABLE_TESTS=ON \
+            -DMUGRID_ENABLE_EXAMPLES=OFF \
+            -DCMAKE_CUDA_ARCHITECTURES="70;80;90"
+          cmake --build build
+
+  # HIP/ROCm compile-only test (no GPU required)
+  hip-compile:
+    runs-on: ubuntu-24.04  # ROCm has better support on 22.04
+    timeout-minutes: 30
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Install ROCm/HIP
+        run: |
+          # Add ROCm repository
+          sudo mkdir -p --mode=0755 /etc/apt/keyrings
+          curl -fsSL https://repo.radeon.com/rocm/rocm.gpg.key | gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
+          echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/6.2.4 jammy main" | sudo tee /etc/apt/sources.list.d/rocm.list > /dev/null
+          # Set package priority to prefer ROCm repo over Ubuntu's packages
+          echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | sudo tee /etc/apt/preferences.d/rocm-pin-600
+          sudo apt-get update -qy
+          # Install HIP development packages (no runtime/driver needed for compile-only)
+          # hipcc: HIP compiler, hip-dev: headers, hipfft: FFT library
+          # rocm-device-libs: device libraries needed by clang for GPU code generation
+          # rocm-cmake: CMake support
+          sudo apt-get install -y \
+            hipcc \
+            hip-dev \
+            hipfft \
+            rocm-device-libs \
+            rocm-cmake
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get install -y \
+            cmake \
+            ninja-build \
+            libboost-test-dev
+
+      - name: Compile with HIP enabled
+        run: |
+          # Set up HIP environment
+          export HIP_PATH=/opt/rocm
+          export PATH=$HIP_PATH/bin:$PATH
+          export CMAKE_PREFIX_PATH=$HIP_PATH:$CMAKE_PREFIX_PATH
+          hipcc --version || echo "hipcc not in PATH, checking /opt/rocm/bin"
+          /opt/rocm/bin/hipcc --version
+          cmake -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DMUGRID_ENABLE_HIP=ON \
+            -DMUGRID_ENABLE_PYTHON=OFF \
+            -DMUGRID_ENABLE_MPI=OFF \
+            -DMUGRID_ENABLE_NETCDF=OFF \
+            -DMUGRID_ENABLE_TESTS=ON \
+            -DMUGRID_ENABLE_EXAMPLES=OFF \
+            -DCMAKE_HIP_ARCHITECTURES="gfx906;gfx908;gfx90a" \
+            -DCMAKE_PREFIX_PATH=/opt/rocm
+          cmake --build build

mugrid-0.0.0/.github/workflows/wheels.yml

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+name: Wheels
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+concurrency:
+  group: wheels-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_wheels:
+    name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    strategy:
+      matrix:
+        buildplat:
+        - [ubuntu-22.04, manylinux, x86_64]
+        - [ubuntu-22.04, manylinux, aarch64]
+        - [macos-14, macosx, arm64]
+        # - [windows-2019, win, AMD64]
+        python: ["cp310", "cp311", "cp312", "cp313", "cp314"]
+      fail-fast: false
+
+    env:
+      IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
+      MACOSX_DEPLOYMENT_TARGET: "${{ matrix.buildplat[0] == 'macos-13' && '13.0' || '14.0' }}"
+
+    steps:
+      - if: matrix.buildplat[2] == 'aarch64'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: all
+          
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.0
+        env:
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_BEFORE_BUILD: bash .github/install_netcdf4.sh
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
+          # Ensure pkg-config can find NetCDF (installed by before-all or before-build)
+          CIBW_ENVIRONMENT_LINUX: PKG_CONFIG_PATH=/usr/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/local/lib/pkgconfig
+          CIBW_ENVIRONMENT_MACOS: >-
+            PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig:/usr/local/lib/pkgconfig
+            PATH=/opt/homebrew/bin:/usr/local/bin:$PATH
+          CIBW_TEST_COMMAND: python3 -c "import muGrid; print(muGrid.__version__); from muGrid._muGrid import FileIONetCDF"
+
+      - uses: actions/upload-artifact@v6
+        with:
+          path: ./wheelhouse/*.whl
+          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
+
+      - name: Check tag
+        id: check-tag
+        run: |
+          if [[ ${{ github.ref }} =~ ^refs/tags/[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+              echo ::set-output name=match::true
+          fi
+        shell: bash
+
+      - name: Deploy to PyPI
+        if: steps.check-tag.outputs.match == 'true'
+        run: |
+          pip install twine
+          twine upload wheelhouse/*.whl
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        shell: bash

mugrid-0.0.0/.gitignore

@@ -0,0 +1,28 @@
+/build/CMake*
+*~
+/build/*
+/build-o3/
+/build*
+/cmake-build-*
+
+/doc/build
+/doc/html
+/doc/xml
+/doc/doxygenxml
+/doc/source/doxygenxml
+/doc/source/html
+
+/venv
+/.venv*/
+
+*.pyc
+
+.fleet
+.vscode
+.idea
+.ccls-cache
+.cache
+
+/subprojects/packagecache/*
+/subprojects/eigen-*/*
+/subprojects/pybind11-*/*

mugrid-0.0.0/.gitmodules

@@ -0,0 +1,11 @@
+[submodule "external/pybind11"]
+	path = external/pybind11
+	url = https://github.com/pybind/pybind11.git
+	branch = stable
+[submodule "external/eigen3"]
+	path = external/eigen3
+	url = https://gitlab.com/libeigen/eigen.git
+	branch = 3.4
+[submodule "external/cork"]
+	path = external/cork
+	url = https://github.com/pastewka/cork

mugrid-0.0.0/.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: https://github.com/pycqa/flake8
+    rev: '7.0.0'
+    hooks:
+    - id: flake8
+      name: flake8 (check python code style)
+  - repo: https://github.com/pycqa/isort
+    rev: '5.13.2'
+    hooks:
+      - id: isort
+        name: isort (check imports)