cad-to-dagmc 0.7.0__tar.gz → 0.7.1__tar.gz

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/.github/workflows/ci_with_benchmarks.yml

@@ -35,11 +35,11 @@ jobs:
           sudo apt-get --allow-releaseinfo-change update
           sudo apt-get update -y
           sudo apt-get upgrade -y
-          sudo apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
+          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
           mamba activate
-          mamba install -y -c conda-forge "openmc=0.14.0=dagmc*nompi*" moab>=5.3.0 gmsh python-gmsh
-          python -m pip install --upgrade pip
-          python -m pip install .
+          mamba install -y -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh
+          python -m ensurepip --upgrade
+          python -m pip install . --no-deps
           python -m pip install openmc_data_downloader
           openmc_data_downloader -l ENDFB-7.1-NNDC -i Fe56 Be9
           git clone --single-branch -b main --depth 1 https://github.com/fusion-energy/model_benchmark_zoo.git

cad_to_dagmc-0.7.0/.github/workflows/ci_with_install.yml → cad_to_dagmc-0.7.1/.github/workflows/ci_with_conda_install.yml

@@ -1,7 +1,7 @@
 
 # This CI does includes particle transport tests as openmc is installed
 
-name: CI with install
+name: CI with Conda install
 
 on:
   pull_request:
@@ -38,15 +38,16 @@ jobs:
           sudo apt-get --allow-releaseinfo-change update
           sudo apt-get update -y
           sudo apt-get upgrade -y
-          sudo apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
+          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
           mamba activate
           mamba create -y --name cad_to_dagmc python=${{ matrix.python-version }}
           mamba activate cad_to_dagmc
-          mamba install -y -c conda-forge "openmc=0.14.0=dagmc*nompi*" gmsh python-gmsh
-          python -m pip install --upgrade pip 
-          python -m pip install .
+          mamba install -y -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh
+          python -m ensurepip --upgrade
+          python -m pip install . --no-deps
           python -c "import cad_to_dagmc"
-          python -m pip install .[tests]
+          mamba install -y -c conda-forge pytest vtk
+          python -m pip install .[tests] --no-deps
           pytest -v tests
           python examples/surface_mesh/cadquery_assembly.py
           python examples/surface_mesh/cadquery_compound.py

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/.github/workflows/ci_with_pip_install.yml

@@ -33,26 +33,19 @@ jobs:
           apt-get --allow-releaseinfo-change update
           apt-get update -y
           apt-get upgrade -y
-          apt-get install -y libgl1-mesa-glx 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 
-          apt-get install -y make cmake
+          apt-get install -y libhdf5-dev 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
           apt install python3
           apt install python3-pip
           python -m pip install --upgrade pip
-          mkdir MOAB
-          cd MOAB
-          git clone --single-branch -b 5.5.1 --depth 1 https://bitbucket.org/fathomteam/moab/
-          mkdir build
-          cd build
-          apt-get install -y libeigen3-dev
-          cmake ../moab -DENABLE_PYMOAB=ON -DENABLE_HDF5=ON -DENABLE_BLASLAPACK=OFF -DENABLE_FORTRAN=OFF
-          make -j2
-          make install
-          cd ../..
-          python -m pip install .
-          python -c "import cad_to_dagmc"
+          git clone  --single-branch -b master --depth 1 https://bitbucket.org/fathomteam/moab/
+          cd moab
+          git checkout faf7e989c0fd0be4a19f61c1d4713afc5397c8a7
+          python -m pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
+          cd ..
+          python -c "import pymoab"
           python -m pip install .[tests]
+          python -c "import cad_to_dagmc"
           pytest -v tests
-          cd examples
           python examples/surface_mesh/cadquery_assembly.py
           python examples/surface_mesh/cadquery_compound.py
           python examples/surface_mesh/cadquery_object_and_stp_file.py

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/.gitignore

@@ -137,3 +137,4 @@ dmypy.json
 *.stp
 src/_version.py
 *.msh
+*.step

cad_to_dagmc-0.7.1/CITATION.cff

@@ -0,0 +1,10 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Shimwell"
+  given-names: "Jonathan"
+  orcid: "https://orcid.org/0000-0001-6909-0946"
+title: "CAD to DAGMC. Convert CAD geometry (STP files) or Cadquery assemblies to DAGMC h5m files"
+version: 0.7.0
+date-released: 2024-4-14
+url: "https://github.com/fusion-energy/cad_to_dagmc"

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cad_to_dagmc
-Version: 0.7.0
+Version: 0.7.1
 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
@@ -15,6 +15,8 @@ License-File: LICENSE
 Requires-Dist: trimesh
 Requires-Dist: networkx
 Requires-Dist: cadquery>=2.4.0
+Requires-Dist: numpy<=1.23.5
+Requires-Dist: gmsh
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: vtk; extra == "tests"
@@ -53,8 +55,6 @@ Also checkout these other software projects that also create DAGMC geometry [CAD
 
 - Install using Mamba
 - Install using Conda
-- Install using Mamba and pip
-- Install using Conda and pip
 - Install using pip and source compilations
 
 ## Install using Mamba
@@ -105,73 +105,32 @@ Then you can install the cad_to_dagmc package
 conda install -y -c conda-forge cad_to_dagmc
 ```
 
-## Install using Mamba and pip
+## Install using pip and source compilations
 
-In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
-- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
-- [Anaconda](https://www.anaconda.com/download)
-- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+It is also possible to avoid the use of conda/mamba and installing using pip.
 
-This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
+First ensure hdf5 is installed as this is needed by MOAB pip install command
 
-Create a new environment, I've chosen Python 3.10 here but newer versions are
-also supported.
-```bash
-mamba create --name new_env python=3.10 -y
 ```
-
-Activate the environment
-```bash
-mamba activate new_env
+sudo apt-get install libhdf5-dev
 ```
 
-Install the dependencies
-```bash
-mamba install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
-```
+Then clone the latest version of MOAB and cd into the moab directory.
 
-Then you can install the cad_to_dagmc package
-```bash
-pip install cad_to_dagmc
 ```
-
-
-## Install using Conda and pip
-
-In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
-- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
-- [Anaconda](https://www.anaconda.com/download)
-- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
-
-This example uses Conda to install some dependencies that are not available via PyPi.
-
-Create a new environment
-```bash
-conda create --name new_env python=3.10 -y
+git clone  master https://bitbucket.org/fathomteam/moab/
+cd moab
 ```
 
-Activate the environment
-```bash
-conda activate new_env
+Ensure pip is up to date as a new version is needed
 ```
-
-Install the dependencies
-```bash
-conda install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
+python -m pip install --upgrade pip
 ```
 
-Then you can install the cad_to_dagmc package
-```bash
-pip install cad_to_dagmc
+Run the pip install command with cmake arguments.
+```
+pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
 ```
-
-## Install using pip and source compilations
-
-It should possible to avoid the use of conda and installing using pip and compiling from source.
-
-First compile MOAB (and install Pymoab) from source
-
-Then install gmsh from source (installing from pip appears to cause conflicts with the open cascade used in ocp and cadquery)
 
 Then you can install the cad_to_dagmc package with ```pip```
 
@@ -199,7 +158,7 @@ The package requires newer versions of Linux. For example the package does not w
 
 The package requires newer versions of pip. It is recommended to ensure that your version of pip is up to date. This can be done with ```python -m pip install --upgrade pip```
 
-Installing one of the package dependancies (gmsh) with pip appears to result in occational errors when passing cad objects between cadquery / ocp and gmsh. The conda install gmsh appears to work fine.
+Installing one of the package dependancies (gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
 
 
 # Usage - creation of DAGMC h5m files

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/README.md

@@ -32,8 +32,6 @@ Also checkout these other software projects that also create DAGMC geometry [CAD
 
 - Install using Mamba
 - Install using Conda
-- Install using Mamba and pip
-- Install using Conda and pip
 - Install using pip and source compilations
 
 ## Install using Mamba
@@ -84,73 +82,32 @@ Then you can install the cad_to_dagmc package
 conda install -y -c conda-forge cad_to_dagmc
 ```
 
-## Install using Mamba and pip
+## Install using pip and source compilations
 
-In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
-- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
-- [Anaconda](https://www.anaconda.com/download)
-- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+It is also possible to avoid the use of conda/mamba and installing using pip.
 
-This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
+First ensure hdf5 is installed as this is needed by MOAB pip install command
 
-Create a new environment, I've chosen Python 3.10 here but newer versions are
-also supported.
-```bash
-mamba create --name new_env python=3.10 -y
 ```
-
-Activate the environment
-```bash
-mamba activate new_env
+sudo apt-get install libhdf5-dev
 ```
 
-Install the dependencies
-```bash
-mamba install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
-```
+Then clone the latest version of MOAB and cd into the moab directory.
 
-Then you can install the cad_to_dagmc package
-```bash
-pip install cad_to_dagmc
 ```
-
-
-## Install using Conda and pip
-
-In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
-- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
-- [Anaconda](https://www.anaconda.com/download)
-- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
-
-This example uses Conda to install some dependencies that are not available via PyPi.
-
-Create a new environment
-```bash
-conda create --name new_env python=3.10 -y
+git clone  master https://bitbucket.org/fathomteam/moab/
+cd moab
 ```
 
-Activate the environment
-```bash
-conda activate new_env
+Ensure pip is up to date as a new version is needed
 ```
-
-Install the dependencies
-```bash
-conda install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
+python -m pip install --upgrade pip
 ```
 
-Then you can install the cad_to_dagmc package
-```bash
-pip install cad_to_dagmc
+Run the pip install command with cmake arguments.
+```
+pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
 ```
-
-## Install using pip and source compilations
-
-It should possible to avoid the use of conda and installing using pip and compiling from source.
-
-First compile MOAB (and install Pymoab) from source
-
-Then install gmsh from source (installing from pip appears to cause conflicts with the open cascade used in ocp and cadquery)
 
 Then you can install the cad_to_dagmc package with ```pip```
 
@@ -178,7 +135,7 @@ The package requires newer versions of Linux. For example the package does not w
 
 The package requires newer versions of pip. It is recommended to ensure that your version of pip is up to date. This can be done with ```python -m pip install --upgrade pip```
 
-Installing one of the package dependancies (gmsh) with pip appears to result in occational errors when passing cad objects between cadquery / ocp and gmsh. The conda install gmsh appears to work fine.
+Installing one of the package dependancies (gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
 
 
 # Usage - creation of DAGMC h5m files

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/examples/unstrucutred_volume_mesh/curved_cadquery_object_to_dagmc_volume_mesh.py

@@ -56,7 +56,7 @@ assembly.save("twist_and_extrude.step")
 
 my_model = CadToDagmc()
 
-my_model.add_cadquery_object(result)
-my_model.add_cadquery_object(result2)
+my_model.add_cadquery_object(result, material_tags=["mat1"])
+my_model.add_cadquery_object(result2, material_tags=["mat2"])
 
 my_model.export_unstructured_mesh_file(filename="umesh.h5m", max_mesh_size=1, min_mesh_size=0.1)

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/pyproject.toml

@@ -21,6 +21,8 @@ dependencies = [
     "trimesh",
     "networkx",
     "cadquery>=2.4.0",
+    "numpy<=1.23.5",
+    "gmsh"
 ]
 dynamic = ["version"]
 

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/src/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.7.0'
-__version_tuple__ = version_tuple = (0, 7, 0)
+__version__ = version = '0.7.1'
+__version_tuple__ = version_tuple = (0, 7, 1)

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/src/cad_to_dagmc/core.py

@@ -1,13 +1,12 @@
-import typing
-
 import cadquery as cq
 import gmsh
 import numpy as np
-from cadquery import importers
+from cadquery import importers, exporters
 from pymoab import core, types
+import tempfile
 
 
-def _define_moab_core_and_tags() -> typing.Tuple[core.Core, dict]:
+def _define_moab_core_and_tags() -> tuple[core.Core, dict]:
     """Creates a MOAB Core instance which can be built up by adding sets of
     triangles to the instance
 
@@ -62,14 +61,11 @@ def _define_moab_core_and_tags() -> typing.Tuple[core.Core, dict]:
 
 
 def _vertices_to_h5m(
-    vertices: typing.Union[
-        typing.Iterable[typing.Tuple[float, float, float]],
-        typing.Iterable["cadquery.occ_impl.geom.Vector"],
-    ],
-    triangles_by_solid_by_face: typing.Iterable[typing.Iterable[typing.Tuple[int, int, int]]],
-    material_tags: typing.Iterable[str],
-    h5m_filename="dagmc.h5m",
-    implicit_complement_material_tag=None,
+    vertices: list[tuple[float, float, float]] | list["cadquery.occ_impl.geom.Vector"],
+    triangles_by_solid_by_face: list[list[tuple[int, int, int]]],
+    material_tags: list[str],
+    h5m_filename: str = "dagmc.h5m",
+    implicit_complement_material_tag: str | None = None,
 ):
     """Converts vertices and triangle sets into a tagged h5m file compatible
     with DAGMC enabled neutronics simulations
@@ -194,8 +190,29 @@ def _vertices_to_h5m(
     return h5m_filename
 
 
+def get_volumes(gmsh, assembly, method="file"):
+
+    if method == "in memory":
+        volumes = gmsh.model.occ.importShapesNativePointer(assembly.wrapped._address())
+        gmsh.model.occ.synchronize()
+    elif method == "file":
+        with tempfile.NamedTemporaryFile(suffix=".step") as temp_file:
+            exporters.export(assembly, temp_file.name)
+            volumes = gmsh.model.occ.importShapes(temp_file.name)
+            gmsh.model.occ.synchronize()
+
+    return gmsh, volumes
+
+
+def init_gmsh():
+    gmsh.initialize()
+    gmsh.option.setNumber("General.Terminal", 1)
+    gmsh.model.add("made_with_cad_to_dagmc_package")
+    return gmsh
+
+
 def _mesh_brep(
-    occ_shape: str,
+    gmsh,
     min_mesh_size: float = 1,
     max_mesh_size: float = 10,
     mesh_algorithm: int = 1,
@@ -219,18 +236,12 @@ def _mesh_brep(
         The resulting gmsh object and volumes
     """
 
-    gmsh.initialize()
-    gmsh.option.setNumber("General.Terminal", 1)
-    gmsh.model.add("made_with_cad_to_dagmc_package")
-    volumes = gmsh.model.occ.importShapesNativePointer(occ_shape)
-    gmsh.model.occ.synchronize()
-
     gmsh.option.setNumber("Mesh.Algorithm", mesh_algorithm)
     gmsh.option.setNumber("Mesh.MeshSizeMin", min_mesh_size)
     gmsh.option.setNumber("Mesh.MeshSizeMax", max_mesh_size)
     gmsh.model.mesh.generate(dimensions)
 
-    return gmsh, volumes
+    return gmsh
 
 
 def mesh_to_vertices_and_triangles(
@@ -336,18 +347,18 @@ class MeshToDagmc:
 
     def export_dagmc_h5m_file(
         self,
-        material_tags: typing.Iterable[str],
-        implicit_complement_material_tag: typing.Optional[str] = None,
+        material_tags: list[str],
+        implicit_complement_material_tag: str | None = None,
         filename: str = "dagmc.h5m",
     ):
         """Saves a DAGMC h5m file of the geometry
 
         Args:
-            material_tags (typing.Iterable[str]): the names of the DAGMC
+            material_tags (list[str]): the names of the DAGMC
                 material tags to assign. These will need to be in the same
                 order as the volumes in the GMESH mesh and match the
                 material tags used in the neutronics code (e.g. OpenMC).
-            implicit_complement_material_tag (typing.Optional[str], optional):
+            implicit_complement_material_tag (str | None, optional):
                 the name of the material tag to use for the implicit
                 complement (void space). Defaults to None which is a vacuum.
             filename (str, optional): _description_. Defaults to "dagmc.h5m".
@@ -395,13 +406,13 @@ class CadToDagmc:
         self,
         filename: str,
         scale_factor: float = 1.0,
-        material_tags: typing.Optional[typing.Iterable[str]] = None,
-    ):
+        material_tags: list[str] | None = None,
+    ) -> int:
         """Loads the parts from stp file into the model.
 
         Args:
             filename: the filename used to save the html graph.
-            material_tags (typing.Iterable[str]): the names of the DAGMC
+            material_tags (list[str]): the names of the DAGMC
                 material tags to assign. These will need to be in the
                 same order as the volumes in the geometry added (STP
                 file and CadQuery objects) and match the material tags
@@ -410,6 +421,9 @@ class CadToDagmc:
                 used to increase the size or decrease the size of the geometry.
                 Useful when converting the geometry to cm for use in neutronics
                 simulations.
+
+        Returns:
+            int: number of volumes in the stp file.
         """
         part = importers.importStep(str(filename)).val()
 
@@ -417,25 +431,28 @@ class CadToDagmc:
             scaled_part = part
         else:
             scaled_part = part.scale(scale_factor)
-        self.add_cadquery_object(cadquery_object=scaled_part, material_tags=material_tags)
+        return self.add_cadquery_object(cadquery_object=scaled_part, material_tags=material_tags)
 
     def add_cadquery_object(
         self,
-        cadquery_object: typing.Union[
-            cq.assembly.Assembly, cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid
-        ],
-        material_tags: typing.Optional[typing.Iterable[str]] = None,
-    ):
+        cadquery_object: (
+            cq.assembly.Assembly | cq.occ_impl.shapes.Compound | cq.occ_impl.shapes.Solid
+        ),
+        material_tags: list[str] | None,
+    ) -> int:
         """Loads the parts from CadQuery object into the model.
 
         Args:
             cadquery_object: the cadquery object to convert, can be a CadQuery assembly
                 cadquery workplane or a cadquery solid
-            material_tags (Optional typing.Iterable[str]): the names of the
+            material_tags (Optional list[str]): the names of the
                 DAGMC material tags to assign. These will need to be in the
                 same order as the volumes in the geometry added (STP file and
                 CadQuery objects) and match the material tags used in the
                 neutronics code (e.g. OpenMC).
+
+        Returns:
+            int: number of volumes in the stp file.
         """
 
         if isinstance(cadquery_object, cq.assembly.Assembly):
@@ -451,12 +468,15 @@ class CadToDagmc:
             self.material_tags = self.material_tags + material_tags
         self.parts = self.parts + iterable_solids
 
+        return len(iterable_solids)
+
     def export_unstructured_mesh_file(
         self,
         filename: str = "umesh.h5m",
         min_mesh_size: float = 1,
         max_mesh_size: float = 5,
         mesh_algorithm: int = 1,
+        method: str = "file",
     ):
 
         assembly = cq.Assembly()
@@ -465,8 +485,12 @@ class CadToDagmc:
 
         imprinted_assembly, _ = cq.occ_impl.assembly.imprint(assembly)
 
-        gmsh, _ = _mesh_brep(
-            occ_shape=imprinted_assembly.wrapped._address(),
+        gmsh = init_gmsh()
+
+        gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method)
+
+        gmsh = _mesh_brep(
+            gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
@@ -491,6 +515,7 @@ class CadToDagmc:
         max_mesh_size: float = 5,
         mesh_algorithm: int = 1,
         dimensions: int = 2,
+        method: str = "file",
     ):
         """Saves a GMesh msh file of the geometry in either 2D surface mesh or
         3D volume mesh.
@@ -502,6 +527,14 @@ class CadToDagmc:
             mesh_algorithm: the gmsh mesh algorithm to use.
             dimensions: The number of dimensions, 2 for a surface mesh 3 for a
                 volume mesh. Passed to gmsh.model.mesh.generate()
+            method: the method to use to import the geometry into gmsh. Options
+                are 'file' or 'in memory'. 'file' is the default and will write
+                the geometry to a temporary file before importing it into gmsh.
+                'in memory' will import the geometry directly into gmsh but
+                requires the version of OpenCASCADE used to build gmsh to be
+                the same as the version used by CadQuery. This is possible to
+                ensure when installing the package with Conda but harder when
+                installing from PyPI.
         """
 
         assembly = cq.Assembly()
@@ -510,8 +543,12 @@ class CadToDagmc:
 
         imprinted_assembly, _ = cq.occ_impl.assembly.imprint(assembly)
 
-        gmsh, _ = _mesh_brep(
-            occ_shape=imprinted_assembly.wrapped._address(),
+        gmsh = init_gmsh()
+
+        gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method)
+
+        gmsh = _mesh_brep(
+            gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
@@ -530,7 +567,8 @@ class CadToDagmc:
         min_mesh_size: float = 1,
         max_mesh_size: float = 5,
         mesh_algorithm: int = 1,
-        implicit_complement_material_tag: typing.Optional[str] = None,
+        implicit_complement_material_tag: str | None = None,
+        method: str = "file",
     ) -> str:
         """Saves a DAGMC h5m file of the geometry
 
@@ -540,10 +578,17 @@ class CadToDagmc:
             min_mesh_size (float, optional): the minimum size of mesh elements to use. Defaults to 1.
             max_mesh_size (float, optional): the maximum size of mesh elements to use. Defaults to 5.
             mesh_algorithm (int, optional): the GMSH mesh algorithm to use.. Defaults to 1.
-            implicit_complement_material_tag (typing.Optional[str], optional):
+            implicit_complement_material_tag (str | None, optional):
                 the name of the material tag to use for the implicit complement
                 (void space). Defaults to None which is a vacuum. Defaults to None.
-
+           method: the method to use to import the geometry into gmsh. Options
+                are 'file' or 'in memory'. 'file' is the default and will write
+                the geometry to a temporary file before importing it into gmsh.
+                'in memory' will import the geometry directly into gmsh but
+                requires the version of OpenCASCADE used to build gmsh to be
+                the same as the version used by CadQuery. This is possible to
+                ensure when installing the package with Conda but harder when
+                installing from PyPI.
         Returns:
             str: the DAGMC filename saved
         """
@@ -570,8 +615,12 @@ class CadToDagmc:
 
         _check_material_tags(material_tags_in_brep_order, self.parts)
 
-        gmsh, volumes = _mesh_brep(
-            occ_shape=imprinted_assembly.wrapped._address(),  # in memory address
+        gmsh = init_gmsh()
+
+        gmsh, volumes = get_volumes(gmsh, imprinted_assembly, method=method)
+
+        gmsh = _mesh_brep(
+            gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/src/cad_to_dagmc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cad_to_dagmc
-Version: 0.7.0
+Version: 0.7.1
 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
@@ -15,6 +15,8 @@ License-File: LICENSE
 Requires-Dist: trimesh
 Requires-Dist: networkx
 Requires-Dist: cadquery>=2.4.0
+Requires-Dist: numpy<=1.23.5
+Requires-Dist: gmsh
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: vtk; extra == "tests"
@@ -53,8 +55,6 @@ Also checkout these other software projects that also create DAGMC geometry [CAD
 
 - Install using Mamba
 - Install using Conda
-- Install using Mamba and pip
-- Install using Conda and pip
 - Install using pip and source compilations
 
 ## Install using Mamba
@@ -105,73 +105,32 @@ Then you can install the cad_to_dagmc package
 conda install -y -c conda-forge cad_to_dagmc
 ```
 
-## Install using Mamba and pip
+## Install using pip and source compilations
 
-In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
-- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
-- [Anaconda](https://www.anaconda.com/download)
-- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+It is also possible to avoid the use of conda/mamba and installing using pip.
 
-This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
+First ensure hdf5 is installed as this is needed by MOAB pip install command
 
-Create a new environment, I've chosen Python 3.10 here but newer versions are
-also supported.
-```bash
-mamba create --name new_env python=3.10 -y
 ```
-
-Activate the environment
-```bash
-mamba activate new_env
+sudo apt-get install libhdf5-dev
 ```
 
-Install the dependencies
-```bash
-mamba install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
-```
+Then clone the latest version of MOAB and cd into the moab directory.
 
-Then you can install the cad_to_dagmc package
-```bash
-pip install cad_to_dagmc
 ```
-
-
-## Install using Conda and pip
-
-In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
-- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
-- [Anaconda](https://www.anaconda.com/download)
-- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
-
-This example uses Conda to install some dependencies that are not available via PyPi.
-
-Create a new environment
-```bash
-conda create --name new_env python=3.10 -y
+git clone  master https://bitbucket.org/fathomteam/moab/
+cd moab
 ```
 
-Activate the environment
-```bash
-conda activate new_env
+Ensure pip is up to date as a new version is needed
 ```
-
-Install the dependencies
-```bash
-conda install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
+python -m pip install --upgrade pip
 ```
 
-Then you can install the cad_to_dagmc package
-```bash
-pip install cad_to_dagmc
+Run the pip install command with cmake arguments.
+```
+pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
 ```
-
-## Install using pip and source compilations
-
-It should possible to avoid the use of conda and installing using pip and compiling from source.
-
-First compile MOAB (and install Pymoab) from source
-
-Then install gmsh from source (installing from pip appears to cause conflicts with the open cascade used in ocp and cadquery)
 
 Then you can install the cad_to_dagmc package with ```pip```
 
@@ -199,7 +158,7 @@ The package requires newer versions of Linux. For example the package does not w
 
 The package requires newer versions of pip. It is recommended to ensure that your version of pip is up to date. This can be done with ```python -m pip install --upgrade pip```
 
-Installing one of the package dependancies (gmsh) with pip appears to result in occational errors when passing cad objects between cadquery / ocp and gmsh. The conda install gmsh appears to work fine.
+Installing one of the package dependancies (gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
 
 
 # Usage - creation of DAGMC h5m files

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/src/cad_to_dagmc.egg-info/SOURCES.txt

@@ -1,11 +1,11 @@
 .gitignore
+CITATION.cff
 LICENSE
 README.md
 pyproject.toml
-.github/workflows/anaconda-publish.yml
 .github/workflows/black.yml
 .github/workflows/ci_with_benchmarks.yml
-.github/workflows/ci_with_install.yml
+.github/workflows/ci_with_conda_install.yml
 .github/workflows/ci_with_pip_install.yml
 .github/workflows/python-publish.yml
 examples/surface_mesh/cadquery_assembly.py
@@ -32,11 +32,9 @@ src/cad_to_dagmc.egg-info/top_level.txt
 tests/ENDFB-7.1-NNDC_H1.h5
 tests/ball_reactor.brep
 tests/curved_extrude.stp
-tests/extrude_rectangle.step
 tests/extrude_rectangle.stp
 tests/multi_volume_cylinders.stp
 tests/one_cube.brep
-tests/single_cube.step
 tests/single_cube.stp
 tests/single_volume_thin.stp
 tests/single_volume_thin.vtk

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/src/cad_to_dagmc.egg-info/requires.txt

@@ -1,6 +1,8 @@
 trimesh
 networkx
 cadquery>=2.4.0
+numpy<=1.23.5
+gmsh
 
 [tests]
 pytest

{cad_to_dagmc-0.7.0 → cad_to_dagmc-0.7.1}/tests/test_python_api.py

@@ -106,3 +106,35 @@ def test_h5m_file_tags():
         2: "mat:mat2",
         3: "mat:mat3",
     }
+
+
+def test_add_cadquery_object_returned_volumes():
+    """Checks that a add_cadquery_object method returns the correct number of volumes"""
+
+    sphere1 = cq.Workplane().sphere(20)
+    sphere2 = cq.Workplane().moveTo(100, 100).sphere(20)
+    sphere3 = cq.Workplane().moveTo(-100, -100).sphere(20)
+
+    c2d = CadToDagmc()
+    vols = c2d.add_cadquery_object(sphere1, material_tags=["mat1"])
+    assert vols == 1
+
+    assembly = cq.Assembly()
+    assembly.add(sphere1)
+    assembly.add(sphere2)
+    assembly.add(sphere3)
+    c2d = CadToDagmc()
+    vols = c2d.add_cadquery_object(assembly, material_tags=["mat1", "mat2", "mat3"])
+    assert vols == 3
+
+
+def test_add_stp_file_returned_volumes():
+    """Checks that a add_stp_file method returns the correct number of volumes"""
+
+    c2d = CadToDagmc()
+    vols = c2d.add_stp_file("tests/curved_extrude.stp")
+    assert vols == 1
+
+    c2d = CadToDagmc()
+    vols = c2d.add_stp_file("tests/two_disconnected_cubes.stp")
+    assert vols == 2

cad_to_dagmc-0.7.0/.github/workflows/anaconda-publish.yml

@@ -1,30 +0,0 @@
-name: anaconda-publish
-
-on:
-  workflow_dispatch:
-  release:
-    types: [published]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    container: continuumio/miniconda3:4.12.0
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up conda
-        run: |
-            apt-get --allow-releaseinfo-change update
-            apt install -y libgl1-mesa-glx
-            conda install -y anaconda-client conda-build
-            conda config --set anaconda_upload no
-      - name: Build and publish to conda
-        env:
-          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        run: |
-            conda build conda -c conda-forge --config-file conda/conda_build_config.yaml
-            conda convert /opt/conda/conda-bld/linux-64/*.tar.bz2 --platform osx-64
-            anaconda upload -f /opt/conda/conda-bld/*/*.tar.bz2
-
-# Note conversion to windows is not supported as MOAB is a dependency