Merge pull request #90 from fusion-energy/catching_failed_in_memory

added try execpt for failed in memory

.github/workflows/ci_with_benchmarks.yml

@@ -18,7 +18,7 @@ on:
 
 jobs:
   testing:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
@@ -37,9 +37,9 @@ jobs:
           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
           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

.github/workflows/ci_with_install.yml → .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:
@@ -20,7 +20,7 @@ on:
 
 jobs:
   testing:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
@@ -42,11 +42,12 @@ jobs:
           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

.github/workflows/ci_with_pip_install.yml

@@ -20,7 +20,7 @@ on:
 
 jobs:
   testing:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     container:
       image: openmc/openmc:develop-dagmc
     steps:
@@ -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-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 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

.gitignore

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

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

examples/unstrucutred_volume_mesh/curved_cadquery_object_to_dagmc_volume_mesh.py

@@ -56,7 +56,7 @@ def gear(t, r1=4, r2=1):
 
 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)

pyproject.toml

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