parosol-py 0.1.3__tar.gz

parosol_py-0.1.3/.github/workflows/build-wheels.yml

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+name: Build Wheels
+
+"on":
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    runs-on: ${{ matrix.os }}
+    permissions:
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            artifact: manylinux-x86_64
+            cibw_arch: x86_64
+          - os: windows-latest
+            artifact: windows-amd64
+            cibw_arch: AMD64
+          - os: macos-latest
+            artifact: macos-arm64
+            cibw_arch: arm64
+          - os: macos-15-intel
+            artifact: macos-x86_64
+            cibw_arch: x86_64
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Cache vcpkg artifacts (Windows)
+        if: matrix.os == 'windows-latest'
+        uses: actions/cache@v4
+        with:
+          path: |
+            C:\vcpkg\downloads
+            C:\vcpkg\buildtrees
+            C:\vcpkg\packages
+            C:\vcpkg\installed
+            C:\vcpkg\bincache
+          key: ${{ runner.os }}-vcpkg-parosol-v1-${{ hashFiles('pyproject.toml', '.github/workflows/build-wheels.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-vcpkg-parosol-v1-
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install --upgrade pip cibuildwheel
+
+      - name: Build wheels (cibuildwheel)
+        env:
+          CIBW_ARCHS: ${{ matrix.cibw_arch }}
+        run: python -m cibuildwheel --output-dir dist
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.artifact }}
+          path: ./dist/*.whl
+
+  build_sdist:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build --sdist --outdir dist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: ./dist/*.tar.gz
+
+  publish:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      id-token: write
+      contents: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/parosol-py
+    steps:
+      - name: Download wheel artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Set up Python for debug tooling
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Debug artifact inventory
+        run: |
+          echo "Current dist/ contents:"
+          ls -lah dist
+          echo
+          echo "Wheel files:"
+          ls -1 dist/*.whl || true
+          echo
+          echo "Source distributions:"
+          ls -1 dist/*.tar.gz || true
+
+      - name: Twine check
+        run: |
+          python -m pip install --upgrade pip twine
+          python -m twine check dist/*
+
+      - name: Upload wheels to GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: |
+            dist/*.whl
+            dist/*.tar.gz
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

parosol_py-0.1.3/.github/workflows/publish-from-run.yml

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+name: Publish From Existing Run
+
+"on":
+  workflow_dispatch:
+    inputs:
+      source_run_id:
+        description: "GitHub Actions run ID that already contains wheels + sdist artifacts"
+        required: true
+        type: string
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+      actions: read
+    environment:
+      name: pypi
+      url: https://pypi.org/p/parosol-py
+    steps:
+      - name: Download wheel artifacts from source run
+        uses: actions/download-artifact@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          repository: ${{ github.repository }}
+          run-id: ${{ inputs.source_run_id }}
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist artifact from source run
+        uses: actions/download-artifact@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          repository: ${{ github.repository }}
+          run-id: ${{ inputs.source_run_id }}
+          name: sdist
+          path: dist
+
+      - name: Set up Python for debug tooling
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Debug artifact inventory
+        run: |
+          echo "Current dist/ contents:"
+          ls -lah dist
+          echo
+          echo "Wheel files:"
+          ls -1 dist/*.whl || true
+          echo
+          echo "Source distributions:"
+          ls -1 dist/*.tar.gz || true
+
+      - name: Twine check
+        run: |
+          python -m pip install --upgrade pip twine
+          python -m twine check dist/*
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

parosol_py-0.1.3/.github/workflows/tests.yml

@@ -0,0 +1,104 @@
+name: Tests
+
+"on":
+  pull_request:
+    branches: ["main", "master"]
+  push:
+    branches: ["main", "master"]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: testenv
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          auto-activate-base: false
+
+      - name: Install native and Python dependencies
+        shell: bash -l {0}
+        run: |
+          conda install -y \
+            cmake \
+            compilers \
+            eigen \
+            hdf5 \
+            make \
+            ninja \
+            numpy \
+            openmpi \
+            pip \
+            pytest \
+            pytest-cov \
+            scikit-build-core \
+            simpleitk
+          python -m pip install --upgrade pip
+          python -m pip install -e . --no-build-isolation
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: pytest -q
+
+  coverage:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: covenv
+          python-version: "3.12"
+          channels: conda-forge
+          auto-activate-base: false
+
+      - name: Install native and Python dependencies
+        shell: bash -l {0}
+        run: |
+          conda install -y \
+            cmake \
+            compilers \
+            eigen \
+            hdf5 \
+            make \
+            ninja \
+            numpy \
+            openmpi \
+            pip \
+            pytest \
+            pytest-cov \
+            scikit-build-core \
+            simpleitk
+          python -m pip install --upgrade pip
+          python -m pip install -e . --no-build-isolation
+
+      - name: Run tests with coverage
+        shell: bash -l {0}
+        run: pytest -q --cov=parosol_py --cov-report=term-missing --cov-report=xml:coverage.xml
+
+      - name: Upload coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml

parosol_py-0.1.3/.gitignore

@@ -0,0 +1,12 @@
+.worktrees/
+docs/superpowers/
+.DS_Store
+.pytest_cache/
+.ruff_cache/
+__pycache__/
+framework-main/
+build/
+dist/
+dist-local-*/
+wheelhouse-*/
+*.egg-info/

parosol_py-0.1.3/CMakeLists.txt

@@ -0,0 +1,7 @@
+cmake_minimum_required(VERSION 3.18)
+project(parosol_py LANGUAGES CXX)
+
+add_subdirectory(src/parosol_native)
+
+install(TARGETS parosol
+        RUNTIME DESTINATION parosol_py/bin)

parosol_py-0.1.3/PKG-INFO

@@ -0,0 +1,153 @@
+Metadata-Version: 2.2
+Name: parosol-py
+Version: 0.1.3
+Summary: Python package and API wrapper for the ParOSol micro-FE solver
+Keywords: finite-element-analysis,bone,hr-pqct,parosol
+Author: Matthias Walle
+Maintainer: Matthias Walle
+License: GPL-2.0-or-later
+Project-URL: Repository, https://github.com/wallematthias/parosol-py
+Project-URL: Native-ParOSol-License, https://github.com/wallematthias/parosol-py/blob/main/src/parosol_native/LICENSE
+Requires-Python: <3.14,>=3.11
+Requires-Dist: numpy>=1.24
+Requires-Dist: h5py>=3.10
+Requires-Dist: SimpleITK>=2.3
+Requires-Dist: aimio-py>=0.1.1
+Requires-Dist: PyYAML>=6
+Requires-Dist: matplotlib>=3.8
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: pytest-cov>=5; extra == "dev"
+Requires-Dist: build>=1; extra == "dev"
+Requires-Dist: cibuildwheel>=2.19; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Provides-Extra: torch
+Requires-Dist: torch>=2.3; extra == "torch"
+Description-Content-Type: text/markdown
+
+# parosol-py
+
+`parosol-py` is the Python package and runtime wrapper for the ParOSol
+micro-FE solver. It provides Python helpers for creating solver inputs, running
+the bundled native executable, reading outputs, and mapping label or density
+images to material stiffness.
+
+The bundled native ParOSol solver was written by Cyril Flaig and is distributed
+under the GNU General Public License, version 2 or later. The Python package is
+therefore distributed as `GPL-2.0-or-later`.
+
+## Install
+
+Prebuilt wheels include the native ParOSol executable:
+
+```bash
+python -m pip install parosol-py
+```
+
+For local development:
+
+```bash
+python -m pip install -e .[dev]
+```
+
+Source installs require CMake, an MPI C++ compiler/runtime, HDF5 C++ libraries,
+and Eigen headers. Release wheels are built for Python 3.11, 3.12, and 3.13.
+macOS wheels currently target macOS 15 or newer because the bundled native
+solver depends on Homebrew HDF5/OpenMPI libraries built for that target.
+
+## Local Check
+
+Before relying on GitHub Actions, run the local verification gate from an
+environment that has the native build tools:
+
+```bash
+python scripts/local_check.py
+```
+
+Add `--smoke-install` to install the built wheel into a temporary virtual
+environment and import it.
+
+## Python API
+
+```python
+import numpy as np
+
+from parosol_py import solve
+
+material = np.ones((10, 10, 10), dtype=np.float32) * 1000.0
+
+result = solve(
+    material=material,
+    spacing=(0.061, 0.061, 0.061),
+    material_unit="MPa",
+    test="axial",
+    test_axis="z",
+    strain=-0.01,
+    outputs=("sed",),
+    export_dir="outputs/example",
+)
+
+print(result.summary)
+print(result.exported)
+```
+
+Use `dry_run=True` to write the ParOSol HDF5 input and command without launching
+the solver:
+
+```python
+result = solve(
+    material=material,
+    spacing=(0.061, 0.061, 0.061),
+    material_unit="MPa",
+    test="axial",
+    test_axis="z",
+    strain=-0.01,
+    dry_run=True,
+    export_dir="outputs/dry_run",
+)
+```
+
+## Material Mapping
+
+Label images can be mapped through an explicit material table:
+
+```python
+import numpy as np
+
+from parosol_py import LinearIsotropicMaterials, labels_to_material_map
+
+labels = np.array([[[100, 127]]], dtype=np.uint16)
+table = LinearIsotropicMaterials(
+    youngs_modulus_mpa={100: 8748.0, 127: 8748.0},
+    poisson_ratio={100: 0.3, 127: 0.3},
+)
+
+mapped = labels_to_material_map(labels, table)
+```
+
+Continuous density images can be converted with one of the supported equations:
+
+```python
+from parosol_py import density_to_material_map
+
+mapped = density_to_material_map(
+    density_image,
+    equation="power",
+    coefficient=10000.0,
+    exponent=1.7,
+    reference_density=1000.0,
+    poisson_ratio=0.3,
+)
+```
+
+The Mulder grayscale BMD law is available as `mulder2007`:
+
+```python
+mapped = density_to_material_map(
+    density_image,
+    equation="mulder2007",
+    active_mask=outer_contour,
+    floor_e_mpa=2.0,
+    poisson_ratio=0.3,
+)
+```

parosol_py-0.1.3/README.md

@@ -0,0 +1,126 @@
+# parosol-py
+
+`parosol-py` is the Python package and runtime wrapper for the ParOSol
+micro-FE solver. It provides Python helpers for creating solver inputs, running
+the bundled native executable, reading outputs, and mapping label or density
+images to material stiffness.
+
+The bundled native ParOSol solver was written by Cyril Flaig and is distributed
+under the GNU General Public License, version 2 or later. The Python package is
+therefore distributed as `GPL-2.0-or-later`.
+
+## Install
+
+Prebuilt wheels include the native ParOSol executable:
+
+```bash
+python -m pip install parosol-py
+```
+
+For local development:
+
+```bash
+python -m pip install -e .[dev]
+```
+
+Source installs require CMake, an MPI C++ compiler/runtime, HDF5 C++ libraries,
+and Eigen headers. Release wheels are built for Python 3.11, 3.12, and 3.13.
+macOS wheels currently target macOS 15 or newer because the bundled native
+solver depends on Homebrew HDF5/OpenMPI libraries built for that target.
+
+## Local Check
+
+Before relying on GitHub Actions, run the local verification gate from an
+environment that has the native build tools:
+
+```bash
+python scripts/local_check.py
+```
+
+Add `--smoke-install` to install the built wheel into a temporary virtual
+environment and import it.
+
+## Python API
+
+```python
+import numpy as np
+
+from parosol_py import solve
+
+material = np.ones((10, 10, 10), dtype=np.float32) * 1000.0
+
+result = solve(
+    material=material,
+    spacing=(0.061, 0.061, 0.061),
+    material_unit="MPa",
+    test="axial",
+    test_axis="z",
+    strain=-0.01,
+    outputs=("sed",),
+    export_dir="outputs/example",
+)
+
+print(result.summary)
+print(result.exported)
+```
+
+Use `dry_run=True` to write the ParOSol HDF5 input and command without launching
+the solver:
+
+```python
+result = solve(
+    material=material,
+    spacing=(0.061, 0.061, 0.061),
+    material_unit="MPa",
+    test="axial",
+    test_axis="z",
+    strain=-0.01,
+    dry_run=True,
+    export_dir="outputs/dry_run",
+)
+```
+
+## Material Mapping
+
+Label images can be mapped through an explicit material table:
+
+```python
+import numpy as np
+
+from parosol_py import LinearIsotropicMaterials, labels_to_material_map
+
+labels = np.array([[[100, 127]]], dtype=np.uint16)
+table = LinearIsotropicMaterials(
+    youngs_modulus_mpa={100: 8748.0, 127: 8748.0},
+    poisson_ratio={100: 0.3, 127: 0.3},
+)
+
+mapped = labels_to_material_map(labels, table)
+```
+
+Continuous density images can be converted with one of the supported equations:
+
+```python
+from parosol_py import density_to_material_map
+
+mapped = density_to_material_map(
+    density_image,
+    equation="power",
+    coefficient=10000.0,
+    exponent=1.7,
+    reference_density=1000.0,
+    poisson_ratio=0.3,
+)
+```
+
+The Mulder grayscale BMD law is available as `mulder2007`:
+
+```python
+mapped = density_to_material_map(
+    density_image,
+    equation="mulder2007",
+    active_mask=outer_contour,
+    floor_e_mpa=2.0,
+    poisson_ratio=0.3,
+)
+```

parosol_py-0.1.3/pyproject.toml

@@ -0,0 +1,71 @@
+[build-system]
+requires = ["scikit-build-core>=0.10"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "parosol-py"
+version = "0.1.3"
+description = "Python package and API wrapper for the ParOSol micro-FE solver"
+readme = "README.md"
+requires-python = ">=3.11,<3.14"
+license = { text = "GPL-2.0-or-later" }
+authors = [{ name = "Matthias Walle" }]
+maintainers = [{ name = "Matthias Walle" }]
+keywords = ["finite-element-analysis", "bone", "hr-pqct", "parosol"]
+dependencies = [
+  "numpy>=1.24",
+  "h5py>=3.10",
+  "SimpleITK>=2.3",
+  "aimio-py>=0.1.1",
+  "PyYAML>=6",
+  "matplotlib>=3.8",
+]
+
+[project.scripts]
+parosol = "parosol_py.cli:main"
+
+[project.urls]
+Repository = "https://github.com/wallematthias/parosol-py"
+Native-ParOSol-License = "https://github.com/wallematthias/parosol-py/blob/main/src/parosol_native/LICENSE"
+
+[project.optional-dependencies]
+dev = [
+  "pytest>=8",
+  "pytest-cov>=5",
+  "build>=1",
+  "cibuildwheel>=2.19",
+  "twine>=5",
+]
+torch = [
+  "torch>=2.3",
+]
+
+[tool.scikit-build]
+cmake.version = ">=3.18"
+wheel.packages = ["src/parosol_py", "src/parosol_torch"]
+
+[tool.cibuildwheel]
+build = "cp311-* cp312-* cp313-*"
+skip = "*-musllinux_* *-manylinux_i686 *-win32"
+test-command = "python -c \"from parosol_py.runner import packaged_executable; p=packaged_executable(); print(p); assert p.exists()\""
+build-verbosity = 1
+
+[tool.cibuildwheel.linux]
+archs = ["x86_64"]
+before-all = "if command -v yum >/dev/null 2>&1; then yum install -y eigen3-devel hdf5-devel openmpi-devel; elif command -v dnf >/dev/null 2>&1; then dnf install -y eigen3-devel hdf5-devel openmpi-devel; elif command -v apt-get >/dev/null 2>&1; then apt-get update && apt-get install -y libeigen3-dev libhdf5-dev libopenmpi-dev openmpi-bin; else echo 'No supported package manager found for native dependencies' && exit 1; fi"
+environment = { PATH="/usr/lib64/openmpi/bin:/usr/lib/openmpi/bin:$PATH", LD_LIBRARY_PATH="/usr/lib64/openmpi/lib:/usr/lib/openmpi/lib:$LD_LIBRARY_PATH" }
+
+[tool.cibuildwheel.macos]
+before-all = "brew install eigen hdf5 open-mpi"
+environment = { CMAKE_PREFIX_PATH="$(brew --prefix eigen):$(brew --prefix hdf5):$(brew --prefix open-mpi)", MACOSX_DEPLOYMENT_TARGET="15.0" }
+repair-wheel-command = "python -m pip install delocate && delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}"
+
+[tool.cibuildwheel.windows]
+archs = ["AMD64"]
+before-all = "powershell -NoProfile -ExecutionPolicy Bypass -Command \"$ErrorActionPreference = 'Stop'; winget install --id Microsoft.msmpi --exact --silent --accept-package-agreements --accept-source-agreements; if (-not (Test-Path 'C:\\Program Files\\Microsoft MPI\\Bin\\mpiexec.exe')) { throw 'MS-MPI redistributable install did not produce mpiexec.exe' }; if (-not (Test-Path 'C:\\vcpkg')) { git clone --depth 1 https://github.com/microsoft/vcpkg C:\\vcpkg }; & C:\\vcpkg\\bootstrap-vcpkg.bat; & C:\\vcpkg\\vcpkg.exe install eigen3:x64-windows hdf5[cpp]:x64-windows msmpi:x64-windows --disable-metrics\""
+environment = { CMAKE_TOOLCHAIN_FILE="C:/vcpkg/scripts/buildsystems/vcpkg.cmake", VCPKG_TARGET_TRIPLET="x64-windows" }
+repair-wheel-command = "python -m pip install delvewheel && delvewheel repair -w {dest_dir} {wheel}"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-ra"