Merge pull request #3 from fusion-energy/adding_ci_for_Examples

added examples ci

.github/workflows/ci_with_examples.yml

@@ -0,0 +1,42 @@
+
+# This CI will launch a Docker image that contains all the dependencies required
+# within that image the pytest test suite is run 
+
+
+name: CI with examples
+
+on:
+  pull_request:    
+    branches:
+    - develop
+    - main
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: continuumio/miniconda3
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: install package
+        run: |
+          pip install .
+      
+      - name: install cadquery as needed by the examples
+        run: |
+          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
+          conda install -c conda-forge mamba
+          mamba install -c conda-forge moab
+          conda install -c cadquery -c conda-forge cadquery=master
+
+      - name: Run examples
+        run: |
+          cd examples
+          python one_volume_cadquery_tesselation.py
+          python one_volume_mesh.py
+          python two_volume_mesh.py

README.md

@@ -3,6 +3,8 @@
 
 [![CI with install](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/ci_with_install.yml/badge.svg)](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/ci_with_install.yml)
 
+[![CI with examples](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/ci_with_examples.yml/badge.svg)](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/ci_with_examples.yml)
+
 [![Upload Python Package](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/python-publish.yml/badge.svg)](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/python-publish.yml)
 [![anaconda-publish](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/anaconda-publish.yml/badge.svg)](https://github.com/fusion-energy/vertices_to_h5m/actions/workflows/anaconda-publish.yml)
 
@@ -52,28 +54,30 @@ material tag mat1.
 
 ```python
 from vertices_to_h5m import vertices_to_h5m
+import numpy as np
 
 # these are the x,y,z coordinates of each vertex. Entries should be floats 
-vertices = np.array([
-    [0., 0., 0.],
-    [1., 0., 0].,
-    [0., 1., 0.],
-    [0., 0., 1.]
-])
+vertices = np.array(
+    [
+        [0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+    ]
+)
+
 
 # These are the triangle that connect individual vertices together to form a continious surface and also a closed volume. Entries should be ints
-triangles = np.array([
-    [0, 1, 2],
-    [3, 1, 2],
-    [0, 2, 3],
-    [0, 1, 3]
-])
+triangles = [
+    np.array([[0, 1, 2], [3, 1, 2], [0, 2, 3], [0, 1, 3]]),
+]
+
 
 # This will produce a h5m file called one_volume.h5m ready for use with DAGMC enabled codes.
 vertices_to_h5m(
     vertices=vertices,
     triangles=triangles,
-    material_tags=["mat1", "mat2"],
+    material_tags=["mat1"],
     h5m_filename="one_volume.h5m",
 )
 ```
@@ -90,14 +94,7 @@ import numpy as np
 
 # These are the x,y,z coordinates of each vertex. Numpy array is set to type float to enforce floats
 vertices = np.array(
-    [
-        [0, 0, 0],
-        [1, 0, 0],
-        [0, 1, 0],
-        [0, 0, 1],
-        [1, 1, 1],
-        [1, 1, 0]
-    ], dtype="float64"
+    [[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1], [1, 1, 1], [1, 1, 0]], dtype="float64"
 )
 
 # These are the two sets triangle that connect individual vertices together to form a continious surfaces and also two closed volume.

conda/meta.yaml

@@ -34,6 +34,8 @@ test:
     - trimesh
     - networkx
     - dagmc_h5m_file_inspector [not win]
+    - openmc
+    - scipy  # trimesh makes use of scipy to fix normals in some cases
   source_files:
     - tests/
   commands:

examples/one_volume_cadquery_tesselation.py

@@ -1,16 +1,19 @@
 import cadquery as cq
+import os
+from vertices_to_h5m import vertices_to_h5m
 
 result = cq.Workplane("front").box(2.0, 2.0, 0.5)
 
+# the inbuild cadquery tessellate does not quite do what is needed for multi
+# parts geometry but work for single part geometry.
+# The cad_to_dagmc package will provide a modified tessellate function in the future
 vertices, triangles = result.val().tessellate(tolerance=0.1)
 
 vertices_to_h5m(
     vertices=vertices,
-    triangles=triangles,
+    triangles=[triangles],
     material_tags=["mat1"],
     h5m_filename="one_cadquery_volume.h5m",
 )
 
-import os
-
 os.system("mbconvert one_cadquery_volume.h5m one_cadquery_volume.vtk")

setup.cfg

@@ -29,13 +29,15 @@ python_requires= >=3.6
 install_requires=
     trimesh
     networkx
+    scipy  # trimesh makes use of scipy to fix normals in some cases
     # moab is also not available on pypi but can be installed with conda
 
 [options.extras_require]
 tests = 
     pytest >= 5.4.3
     dagmc_h5m_file_inspector # requires moab which can be installed with conda
     openmc_data_downloader
+    # openmc is also needed but not available via pip
 
 [flake8]
 per-file-ignores = __init__.py:F401

tests/test_package.py

@@ -16,8 +16,7 @@
 
 
 def transport_particles_on_h5m_geometry(
-    h5m_filename,
-    material_tags,
+    h5m_filename, material_tags, cross_sections_xml=None
 ):
     """A function for testing the geometry file with particle transport in DAGMC OpenMC"""
 
@@ -31,9 +30,8 @@ def transport_particles_on_h5m_geometry(
 
         materials.append(mat_dag_material_tag)
 
-    materials.cross_sections = (
-        "/home/jshim/brep_to_h5m/examples/h5m_from_coords/cross_sections.xml"
-    )
+    if cross_sections_xml:
+        materials.cross_sections = cross_sections_xml
     # downloads the nuclear data and sets the openmc_cross_sections environmental variable
     odd.just_in_time_library_generator(libraries="ENDFB-7.1-NNDC", materials=materials)
 

vertices_to_h5m/core.py

@@ -1,4 +1,4 @@
-from typing import Iterable, Tuple
+from typing import Iterable, Tuple, Union
 
 import numpy as np
 import trimesh
@@ -148,17 +148,42 @@ def add_triangles_to_moab_core(
 
 
 def vertices_to_h5m(
-    vertices: Iterable[Tuple[float, float, float]],
+    vertices: Union[
+        Iterable[Tuple[float, float, float]], Iterable["cadquery.occ_impl.geom.Vector"]
+    ],
     triangles: Iterable[Tuple[int, int, int]],
     material_tags: Iterable[str],
     h5m_filename="dagmc.h5m",
 ):
+    """Converts vertices and triangle sets into a tagged h5m file compatible
+    with DAGMC enabled neutronics simulations
+
+    Args:
+        vertices:
+        triangles:
+        material_tags:
+        h5m_filename:
+    """
 
     if len(material_tags) != len(triangles):
         msg = f"The number of material_tags provided is {len(material_tags)} and the number of sets of triangles is {len(triangles)}. You must provide one material_tag for every triangle set"
         raise ValueError(msg)
 
-    triangles = fix_normals(vertices=vertices, triangles_in_each_volume=triangles)
+    # limited attribute checking to see if user passed in a list of CadQuery vectors
+    if (
+        hasattr(vertices[0], "x")
+        and hasattr(vertices[0], "y")
+        and hasattr(vertices[0], "z")
+    ):
+        vertices_floats = []
+        for vert in vertices:
+            vertices_floats.append((vert.x, vert.y, vert.z))
+    else:
+        vertices_floats = vertices
+
+    triangles = fix_normals(
+        vertices=vertices_floats, triangles_in_each_volume=triangles
+    )
 
     moab_core, tags = _define_moab_core_and_tags()
 
@@ -168,7 +193,7 @@ def vertices_to_h5m(
         )
 
         moab_core, moab_verts = add_vertices_to_moab_core(
-            moab_core, vertices, surface_set
+            moab_core, vertices_floats, surface_set
         )
 
         moab_core = add_triangles_to_moab_core(