cad-to-dagmc 0.10.0__tar.gz → 0.11.0__tar.gz

{cad_to_dagmc-0.10.0 → cad_to_dagmc-0.11.0}/.github/workflows/ci_with_conda_install.yml

@@ -69,6 +69,7 @@ jobs:
           source "${HOME}/miniforge/etc/profile.d/conda.sh"
           conda activate ci-env
           python examples/surface_mesh/cadquery_assembly.py
+          python examples/surface_mesh/cadquery_assembly_with_different_h5m_backends.py
           python examples/surface_mesh/cadquery_assembly_with_materials.py
           python examples/surface_mesh/cadquery_assembly_with_names.py
           python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py

{cad_to_dagmc-0.10.0 → cad_to_dagmc-0.11.0}/.github/workflows/ci_with_pip_install.yml

@@ -1,5 +1,6 @@
 
-# This CI does not currently include particle transport tests as openmc is not installed
+# This CI tests the package with both h5py-only (for users without pymoab)
+# and with pymoab (full functionality)
 
 name: CI with pip install
 
@@ -32,22 +33,46 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: install non pypi dependencies
+      - name: Install system dependencies
         shell: bash
         run: |
           sudo apt-get update -y
           sudo apt-get upgrade -y
           sudo apt-get install -y libblas-dev liblapack-dev libgl1 libglx-mesa0 libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0 libxcursor-dev libxft2 libxinerama-dev make cmake libeigen3-dev
-          # Python3 and pip are pre-installed on GitHub Actions runners
-          python -m pip install --extra-index-url https://shimwell.github.io/wheels moab openmc
+
+      - name: Install package and openmc (without pymoab)
+        shell: bash
+        run: |
           # install the latest cadquery master branch as it has PR https://github.com/CadQuery/cadquery/pull/1923 merged in
           python -m pip install git+https://github.com/CadQuery/cadquery
-          python -c "import pymoab"
+          # Install openmc without moab - openmc tests will be skipped if DAGMC not available
+          python -m pip install --extra-index-url https://shimwell.github.io/wheels openmc
           python -m pip install .[tests]
-          python -m pip install git+https://github.com/svalinn/pydagmc
           python -c "import cad_to_dagmc"
+
+      - name: Run tests with h5py backend only (validates package works without pymoab)
+        shell: bash
+        run: |
+          # pymoab tests will be automatically skipped by conftest.py
+          pytest -v tests
+
+      - name: Install pymoab
+        shell: bash
+        run: |
+          python -m pip install --extra-index-url https://shimwell.github.io/wheels moab
+          python -c "import pymoab"
+          python -m pip install git+https://github.com/svalinn/pydagmc
+
+      - name: Run full tests with both backends
+        shell: bash
+        run: |
           pytest -v tests
+
+      - name: Run examples
+        shell: bash
+        run: |
           python examples/surface_mesh/cadquery_assembly.py
+          python examples/surface_mesh/cadquery_assembly_with_different_h5m_backends.py
           python examples/surface_mesh/cadquery_assembly_with_materials.py
           python examples/surface_mesh/cadquery_assembly_with_names.py
           python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py

cad_to_dagmc-0.11.0/.github/workflows/docs.yml

@@ -0,0 +1,78 @@
+name: Documentation
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install system packages
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libgl1 libglx-mesa0 libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[docs,tests]
+
+      - name: Test documentation code snippets
+        run: |
+          pytest --codeblocks docs/ --ignore=docs/_build
+
+      - name: Build documentation (tagged version)
+        if: startsWith(github.ref, 'refs/tags/')
+        run: |
+          sphinx-build docs _build/${{ github.ref_name }}
+          # Also build as 'stable' for latest tagged release
+          sphinx-build docs _build/stable
+
+      - name: Build documentation (dev version)
+        if: github.event_name == 'push' && !startsWith(github.ref, 'refs/tags/')
+        run: |
+          sphinx-build docs _build/dev
+
+      - name: Build documentation (PR check)
+        if: github.event_name == 'pull_request'
+        run: |
+          sphinx-build docs _build/pr-${{ github.event.pull_request.number }}
+
+      - name: Check links
+        if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/')
+        run: |
+          sphinx-build -b linkcheck docs _build/linkcheck || true
+
+      - name: Add root redirect
+        if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/')
+        run: |
+          cp docs/_static/root_redirect.html _build/index.html
+
+      - name: Deploy to GitHub Pages
+        if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/')
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build
+          keep_files: true

cad_to_dagmc-0.11.0/PKG-INFO

@@ -0,0 +1,56 @@
+Metadata-Version: 2.4
+Name: cad_to_dagmc
+Version: 0.11.0
+Summary: Converts CAD files to a DAGMC h5m file
+Author-email: Jonathan Shimwell <mail@jshimwell.com>
+Project-URL: Homepage, https://github.com/fusion-energy/cad_to_dagmc
+Project-URL: Bug Tracker, https://github.com/fusion-energy/cad_to_dagmc/issues
+Keywords: dagmc,geometry,plot,slice
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: trimesh
+Requires-Dist: networkx
+Requires-Dist: cadquery>=2.6.0
+Requires-Dist: numpy
+Requires-Dist: gmsh
+Requires-Dist: h5py
+Requires-Dist: cadquery_direct_mesh_plugin>=0.1.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-codeblocks; extra == "tests"
+Requires-Dist: vtk; extra == "tests"
+Requires-Dist: assembly-mesh-plugin; extra == "tests"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-book-theme; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid; extra == "docs"
+Requires-Dist: sphinxcadquery; extra == "docs"
+Requires-Dist: pyvista[jupyter]; extra == "docs"
+Requires-Dist: panel; extra == "docs"
+Requires-Dist: jupyter-sphinx; extra == "docs"
+Dynamic: license-file
+
+
+[![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
+
+[![CI with Conda install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_conda_install.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_conda_install.yml) Testing package and running examples with dependencies installed via Conda
+
+[![CI with pip install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_pip_install.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_pip_install.yml) Testing package and running examples with dependencies installed via pip
+
+[![CI with model benchmark zoo](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_benchmarks.yml/badge.svg?branch=main)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_benchmarks.yml) Testing with [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo)
+
+[![Upload Python Package](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/python-publish.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/python-publish.yml)
+
+[![PyPI](https://img.shields.io/pypi/v/cad_to_dagmc?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/cad_to_dagmc/)
+
+
+A minimal package that converts CAD geometry to [DAGMC](https://github.com/svalinn/DAGMC/) (h5m) files, [unstructured mesh](https://docs.openmc.org/en/latest/pythonapi/generated/openmc.UnstructuredMesh.html) files (vtk) and Gmsh (msh) files ready for use in neutronics simulations.
+
+## See the :point_right: [online documentation](https://fusion-energy.github.io/cad_to_dagmc/) :point_left: for installation options, usage recommendations and Python API details.

cad_to_dagmc-0.11.0/README.md

@@ -0,0 +1,17 @@
+
+[![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
+
+[![CI with Conda install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_conda_install.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_conda_install.yml) Testing package and running examples with dependencies installed via Conda
+
+[![CI with pip install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_pip_install.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_pip_install.yml) Testing package and running examples with dependencies installed via pip
+
+[![CI with model benchmark zoo](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_benchmarks.yml/badge.svg?branch=main)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_benchmarks.yml) Testing with [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo)
+
+[![Upload Python Package](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/python-publish.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/python-publish.yml)
+
+[![PyPI](https://img.shields.io/pypi/v/cad_to_dagmc?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/cad_to_dagmc/)
+
+
+A minimal package that converts CAD geometry to [DAGMC](https://github.com/svalinn/DAGMC/) (h5m) files, [unstructured mesh](https://docs.openmc.org/en/latest/pythonapi/generated/openmc.UnstructuredMesh.html) files (vtk) and Gmsh (msh) files ready for use in neutronics simulations.
+
+## See the :point_right: [online documentation](https://fusion-energy.github.io/cad_to_dagmc/) :point_left: for installation options, usage recommendations and Python API details.

cad_to_dagmc-0.11.0/docs/Makefile

@@ -0,0 +1,14 @@
+# Minimal makefile for Sphinx documentation
+
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

cad_to_dagmc-0.11.0/docs/_static/custom.css

@@ -0,0 +1,67 @@
+/* Custom styles for cad_to_dagmc documentation */
+
+/* Mermaid diagram styling */
+.mermaid {
+    text-align: center;
+    margin: 1em auto;
+    padding: 0.5em;
+    background: linear-gradient(135deg, #fafafa 0%, #f5f5f5 100%);
+    border-radius: 12px;
+    max-width: 100%;
+    overflow-x: auto;
+}
+
+.mermaid svg {
+    max-width: 100%;
+    max-height: 280px;
+    height: auto;
+}
+
+/* Code block styling */
+div.highlight {
+    border-radius: 8px;
+    overflow: hidden;
+}
+
+div.highlight pre {
+    font-size: 0.875em;
+    line-height: 1.6;
+    padding: 1em;
+    margin: 0;
+}
+
+/* Inline code */
+code.literal {
+    background: #f1f5f9;
+    padding: 2px 6px;
+    border-radius: 4px;
+    font-size: 0.9em;
+}
+
+/* Table styling */
+table {
+    width: 100%;
+}
+
+/* Admonition styling */
+.admonition {
+    margin: 1.5em 0;
+    padding: 1em 1.25em;
+    border-radius: 8px;
+    border-left: 4px solid;
+}
+
+.admonition.note {
+    background: #eff6ff;
+    border-left-color: #3b82f6;
+}
+
+.admonition.warning {
+    background: #fefce8;
+    border-left-color: #eab308;
+}
+
+.admonition-title {
+    font-weight: 600;
+    margin-bottom: 0.5em;
+}

cad_to_dagmc-0.11.0/docs/_static/root_redirect.html

@@ -0,0 +1,10 @@
+<!DOCTYPE html>
+<html>
+<head>
+    <meta http-equiv="refresh" content="0; url=dev/" />
+    <script>window.location.href = "dev/";</script>
+</head>
+<body>
+    <p>Redirecting to <a href="dev/">documentation</a>...</p>
+</body>
+</html>

cad_to_dagmc-0.11.0/docs/advanced.md

@@ -0,0 +1,218 @@
+# Advanced Options
+
+This page covers advanced configuration options.
+
+## Geometry Scaling
+
+Scale geometry using the `scale_factor` parameter. Useful when converting
+between units (e.g., mm to cm for neutronics).
+
+<!--pytest-codeblocks:skip-->
+```python
+# Scale from mm to cm (divide by 10)
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    scale_factor=0.1,
+)
+
+# Scale up by 2x
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    scale_factor=2.0,
+)
+```
+
+## Per-Volume Mesh Sizing
+
+Set different mesh sizes for different volumes using `set_size`.
+
+<!--pytest-codeblocks:skip-->
+```python
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    min_mesh_size=1.0,
+    max_mesh_size=10.0,
+    set_size={
+        1: 0.5,   # Volume 1: fine mesh (0.5)
+        2: 5.0,   # Volume 2: coarse mesh (5.0)
+        3: 1.0,   # Volume 3: medium mesh (1.0)
+    }
+)
+```
+
+:::{note}
+`set_size` only works with the GMSH meshing backend.
+:::
+
+## Mesh Algorithms
+
+GMSH provides multiple meshing algorithms. Select with `mesh_algorithm`.
+
+<!--pytest-codeblocks:skip-->
+```python
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    mesh_algorithm=6,  # Frontal-Delaunay
+)
+```
+
+**Available algorithms:**
+
+- `1`: MeshAdapt (default)
+- `2`: Automatic
+- `5`: Delaunay
+- `6`: Frontal-Delaunay
+- `7`: BAMG
+- `8`: Frontal-Delaunay for Quads
+- `9`: Packing of Parallelograms
+
+See [GMSH documentation](https://gmsh.info/doc/texinfo/gmsh.html#Mesh-options)
+for details.
+
+## Imprinting Control
+
+Imprinting ensures shared surfaces between adjacent volumes are meshed consistently.
+It's enabled by default but can be disabled for geometries that don't need it.
+
+<!--pytest-codeblocks:skip-->
+```python
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    imprint=False,  # Disable imprinting
+)
+```
+
+:::{warning}
+Disabling imprinting may cause mesh inconsistencies at volume interfaces.
+Only disable if you know your geometry doesn't require it.
+:::
+
+## CAD Transfer Method
+
+Control how CAD geometry is transferred to GMSH.
+
+<!--pytest-codeblocks:skip-->
+```python
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    method="file",      # Write to temp file (default, more compatible)
+    # or
+    method="inMemory",  # Direct transfer (faster, requires matching OCC versions)
+)
+```
+
+**File method (default):**
+
+- More compatible across installations
+- Works with pip-installed packages
+- Slightly slower due to file I/O
+
+**In-memory method:**
+
+- Faster for large geometries
+- Requires matching OpenCASCADE versions between CadQuery and GMSH
+- Works reliably with Conda installations
+
+## Implicit Complement Material
+
+Set a material tag for DAGMC's implicit complement (the void space).
+
+<!--pytest-codeblocks:skip-->
+```python
+my_model.export_dagmc_h5m_file(
+    filename="dagmc.h5m",
+    implicit_complement_material_tag="void",
+)
+```
+
+## Accessing the GMSH Object
+
+For advanced mesh control, access the GMSH object directly.
+
+<!--pytest-codeblocks:skip-->
+```python
+import gmsh
+import cad_to_dagmc
+
+# Initialize GMSH
+gmsh_obj = cad_to_dagmc.init_gmsh()
+
+# ... add geometry and configure mesh ...
+
+# Set advanced GMSH options
+gmsh.option.setNumber("Mesh.OptimizeNetgen", 1)
+gmsh.option.setNumber("Mesh.Smoothing", 5)
+
+# Generate mesh
+gmsh.model.mesh.generate(2)
+
+# Export
+cad_to_dagmc.export_gmsh_object_to_dagmc_h5m_file(filename="dagmc.h5m")
+
+gmsh.finalize()
+```
+
+## Parallel Processing
+
+Both CadQuery and GMSH use parallel processing for operations like imprinting and meshing.
+By default, they use all available CPU cores. On shared servers or when memory is limited,
+you may want to restrict the number of threads.
+
+### Limiting CadQuery Threads
+
+CadQuery provides a `setThreads` function to control the number of threads used for
+boolean operations and imprinting:
+
+<!--pytest-codeblocks:skip-->
+```python
+from cadquery.occ_impl.shapes import setThreads
+
+setThreads(4)  # Limit to 4 threads
+```
+
+This can be called at any point before your geometry operations.
+
+Alternatively, you can configure the thread pool before importing CadQuery:
+
+<!--pytest-codeblocks:skip-->
+```python
+import OCP
+OCP.OSD.OSD_ThreadPool.DefaultPool_s(4)  # Limit to 4 threads
+
+import cadquery as cq
+from cad_to_dagmc import CadToDagmc
+```
+
+Or use the `OMP_NUM_THREADS` environment variable:
+
+<!--pytest-codeblocks:skip-->
+```bash
+export OMP_NUM_THREADS=4
+python my_script.py
+```
+
+### Limiting GMSH Threads
+
+GMSH parallelism is controlled through its own options:
+
+<!--pytest-codeblocks:skip-->
+```python
+import gmsh
+import cad_to_dagmc
+
+gmsh_obj = cad_to_dagmc.init_gmsh()
+
+# Limit parallel meshing to 4 threads
+gmsh.option.setNumber("General.NumThreads", 4)
+gmsh.option.setNumber("Mesh.MaxNumThreads1D", 4)
+gmsh.option.setNumber("Mesh.MaxNumThreads2D", 4)
+gmsh.option.setNumber("Mesh.MaxNumThreads3D", 4)
+
+# ... continue with meshing ...
+```
+
+### When to Limit Threads
+
+- **Shared servers**: Avoid monopolizing all cores
+- **Memory constraints**: Each thread requires memory; fewer threads = lower peak memory
+- **Debugging**: Single-threaded execution can make errors easier to diagnose

cad_to_dagmc-0.11.0/docs/api.md

@@ -0,0 +1,51 @@
+# Python API Reference
+
+## Main Class
+
+```{eval-rst}
+.. autoclass:: cad_to_dagmc.CadToDagmc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## Standalone Functions
+
+### GMSH to DAGMC Conversion
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.export_gmsh_file_to_dagmc_h5m_file
+```
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.export_gmsh_object_to_dagmc_h5m_file
+```
+
+### Low-Level Functions
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.vertices_to_h5m
+```
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.init_gmsh
+```
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.get_volumes
+```
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.set_sizes_for_mesh
+```
+
+```{eval-rst}
+.. autofunction:: cad_to_dagmc.mesh_to_vertices_and_triangles
+```
+
+## Exceptions
+
+```{eval-rst}
+.. autoexception:: cad_to_dagmc.PyMoabNotFoundError
+   :show-inheritance:
+```