From b19a0b186d1557d7ca506c9402908010e1c96d89 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Sat, 30 Jul 2022 23:03:01 +0100
Subject: [PATCH 01/17] added test yml

---
 .github/workflows/ci_with_install.yml | 44 +++++++++++++++++++++++++++
 cad_to_dagmc/core.py                  | 10 ------
 tests/test_package.py                 |  2 +-
 3 files changed, 45 insertions(+), 11 deletions(-)
 create mode 100644 .github/workflows/ci_with_install.yml

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
new file mode 100644
index 0000000..5dcc331
--- /dev/null
+++ b/.github/workflows/ci_with_install.yml
@@ -0,0 +1,44 @@
+
+# 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 install
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+    paths-ignore:
+      - 'docs/**'
+      - '.gitignore'
+      - '*.md'
+      - 'CITATION.cff'
+      - 'LICENSE.txt'
+      - 'readthedocs.yml'
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: openmc/openmc:develop
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: install package
+        run: |
+          pip install .
+          python -c "import cad_to_dagmc"
+
+      # - name: Run examples
+      #   run: |
+      #     python examples/
+
+      - name: Run tests
+        run: |
+          pip install .[tests]
+          pytest tests -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
+
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v2
diff --git a/cad_to_dagmc/core.py b/cad_to_dagmc/core.py
index b28db69..af3e080 100644
--- a/cad_to_dagmc/core.py
+++ b/cad_to_dagmc/core.py
@@ -1,17 +1,7 @@
 from vertices_to_h5m import vertices_to_h5m
 from pathlib import Path
-import dagmc_h5m_file_inspector as di
-import openmc
-import openmc_data_downloader as odd
 import math
 
-"""
-Tests that check that:
-    - h5m files are created
-    - h5m files contain the correct number of volumes
-    - h5m files contain the correct material tags
-    - h5m files can be used a transport geometry in DAGMC with OpenMC
-"""
 
 
 from cadquery import importers
diff --git a/tests/test_package.py b/tests/test_package.py
index 901f31a..0a7e680 100644
--- a/tests/test_package.py
+++ b/tests/test_package.py
@@ -1,6 +1,6 @@
 from vertices_to_h5m import vertices_to_h5m
 from pathlib import Path
-import dagmc_h5m_file_inspector as di
+# import dagmc_h5m_file_inspector as di
 import openmc
 import openmc_data_downloader as odd
 import math

From 73015fd65eb03069a3371b32a87bec0971c8eb92 Mon Sep 17 00:00:00 2001
From: shimwell <shimwell@users.noreply.github.com>
Date: Sat, 30 Jul 2022 22:03:44 +0000
Subject: [PATCH 02/17] [skip ci] Apply formatting changes

---
 cad_to_dagmc/core.py  | 1 -
 tests/test_package.py | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/cad_to_dagmc/core.py b/cad_to_dagmc/core.py
index af3e080..83c3933 100644
--- a/cad_to_dagmc/core.py
+++ b/cad_to_dagmc/core.py
@@ -3,7 +3,6 @@
 import math
 
 
-
 from cadquery import importers
 from OCP.GCPnts import GCPnts_QuasiUniformDeflection
 
diff --git a/tests/test_package.py b/tests/test_package.py
index 0a7e680..01809a4 100644
--- a/tests/test_package.py
+++ b/tests/test_package.py
@@ -1,5 +1,6 @@
 from vertices_to_h5m import vertices_to_h5m
 from pathlib import Path
+
 # import dagmc_h5m_file_inspector as di
 import openmc
 import openmc_data_downloader as odd

From 3116f7e4fefe1725d15bb518361fa3896cf13abc Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Sat, 30 Jul 2022 23:09:52 +0100
Subject: [PATCH 03/17] added python publish ci

---
 .github/workflows/python-publish.yml | 40 ++++++++++++++++++++++++++++
 README.md                            |  8 +++++-
 2 files changed, 47 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/python-publish.yml

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
new file mode 100644
index 0000000..ac5bbec
--- /dev/null
+++ b/.github/workflows/python-publish.yml
@@ -0,0 +1,40 @@
+# This yml file will trigger a Github Actions event that builds and upload the
+# Python package to PiPy. This makes use of Twine and is triggered when a push
+# to the main branch occures. For more information see:
+# https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# and for details on the Autobump version section see:
+# https://github.com/grst/python-ci-versioneer
+
+name: Upload Python Package
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel build twine
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python -m build
+        twine check dist/*
+        twine upload dist/*
diff --git a/README.md b/README.md
index a864f9c..ca22752 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,12 @@
-# cad_to_dagmc
+
 A minimal package that uses CadQuery functionality to convert Cad geometry to DAGMC h5m files
 
+# Install
+
+```bash
+pip install cad_to_dagmc
+```
+
 # Usage
 
 ```python

From 0d230601ea81edcb28ddda808b544cb8273a0a0e Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Sat, 30 Jul 2022 23:14:58 +0100
Subject: [PATCH 04/17] change docker image

---
 .github/workflows/ci_with_install.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 5dcc331..f30cb47 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -21,7 +21,7 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     container:
-      image: openmc/openmc:develop
+      image: openmc/openmc:develop-dagmc
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2

From 4079ab19fae50d51bcaf35d70725af4c1a109e3e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 09:59:24 +0100
Subject: [PATCH 05/17] added moab to ci env

---
 .github/workflows/ci_with_install.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index f30cb47..ddf8770 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -31,9 +31,10 @@ jobs:
           pip install .
           python -c "import cad_to_dagmc"
 
-      # - name: Run examples
-      #   run: |
-      #     python examples/
+      - name: install non pypi dependencies
+        run: |
+          conda install -c conda-forge mamba
+          mamba install -c conda-forge moab
 
       - name: Run tests
         run: |

From 5328e6350f99f3527aff1a4bb8a449b87bb5a9da Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 10:03:59 +0100
Subject: [PATCH 06/17] moab==5.3.1

---
 .github/workflows/ci_with_install.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index ddf8770..6c97b07 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -34,7 +34,7 @@ jobs:
       - name: install non pypi dependencies
         run: |
           conda install -c conda-forge mamba
-          mamba install -c conda-forge moab
+          mamba install -c conda-forge moab==5.3.1
 
       - name: Run tests
         run: |

From 9730e43565d08247d5f003e7cabda5934c8be3f3 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 10:19:23 +0100
Subject: [PATCH 07/17] trying mamba env for all

---
 .github/workflows/ci_with_install.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 6c97b07..140e047 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -21,7 +21,7 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     container:
-      image: openmc/openmc:develop-dagmc
+      image: continuumio/miniconda3:4.12.0
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -34,7 +34,8 @@ jobs:
       - name: install non pypi dependencies
         run: |
           conda install -c conda-forge mamba
-          mamba install -c conda-forge moab==5.3.1
+          mamba install -c conda-forge openmc
+          mamba install -c cadquery -c conda-forge cadquery=master
 
       - name: Run tests
         run: |

From 2495c784afecf1f614fa2a7f5e5533aa5a73e7df Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 10:22:27 +0100
Subject: [PATCH 08/17] moving order of package install

---
 .github/workflows/ci_with_install.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 140e047..d4d125c 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -26,20 +26,20 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: install package
-        run: |
-          pip install .
-          python -c "import cad_to_dagmc"
-
       - name: install non pypi dependencies
         run: |
           conda install -c conda-forge mamba
-          mamba install -c conda-forge openmc
           mamba install -c cadquery -c conda-forge cadquery=master
 
+      - name: install package
+        run: |
+          pip install .
+          python -c "import cad_to_dagmc"
+
       - name: Run tests
         run: |
           pip install .[tests]
+          mamba install -c conda-forge openmc
           pytest tests -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
 
       - name: Upload to codecov

From 6f042c9542724a6ed359bf6aaa25c8f5d257b953 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 10:40:50 +0100
Subject: [PATCH 09/17] added moab

---
 .github/workflows/ci_with_install.yml |  1 +
 README.md                             | 19 ++++++++++++++++++-
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index d4d125c..481bbcb 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -29,6 +29,7 @@ jobs:
       - name: install non pypi dependencies
         run: |
           conda install -c conda-forge mamba
+          mamba install -c conda-forge moab
           mamba install -c cadquery -c conda-forge cadquery=master
 
       - name: install package
diff --git a/README.md b/README.md
index ca22752..c8f9433 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,23 @@
-
 A minimal package that uses CadQuery functionality to convert Cad geometry to DAGMC h5m files
 
+This particular method of producing DAGMC compatible h5m files from CAD geometry
+is intended to convert STP files or [CadQuery](https://cadquery.readthedocs.io) objects to h5m file.
+
+The use of CadQuery based surface tesselation and then conversion of the
+vertices and triangle sets into h5m files directly (in memory) is relatively
+fast with minimal file IO and the resulting meshed volumes have low triangle
+count while maintaining a good representation of the volume as described in
+[this](https://www.sciencedirect.com/science/article/abs/pii/S0920379615301484)
+publication.
+
+While this package concentrates on loading the CAD and meshing the surface it
+then hands off the vertices and triangles sets to
+[vertices_to_h5m](https://github.com/fusion-energy/vertices_to_h5m) which
+converts these into a h5m geometry file.
+Due to the modularity of this workflow if you have a preferred meshing
+algorithm then it is entirely possible to pipe your own vertices and triangles
+directly into vertices_to_h5m.
+
 # Install
 
 ```bash

From e46a76fcd0b2ffff54131ec6449910dc925c53c5 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 10:44:12 +0100
Subject: [PATCH 10/17] added libgl to container

---
 .github/workflows/ci_with_install.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 481bbcb..10e4216 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -28,6 +28,10 @@ jobs:
 
       - name: install non pypi dependencies
         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
           mamba install -c cadquery -c conda-forge cadquery=master
@@ -40,7 +44,7 @@ jobs:
       - name: Run tests
         run: |
           pip install .[tests]
-          mamba install -c conda-forge openmc
+          mamba install -c conda-forge -y "openmc=0.13.0=dagmc*nompi*"
           pytest tests -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
 
       - name: Upload to codecov

From 079813da5a2ab26f0fae350724baa9626653a433 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 12:05:28 +0100
Subject: [PATCH 11/17] split tests into creation and transport

---
 tests/test_h5m_creation.py                    | 85 ++++++++++++++++++
 ...t_package.py => test_h5m_in_simulation.py} | 89 +++----------------
 2 files changed, 97 insertions(+), 77 deletions(-)
 create mode 100644 tests/test_h5m_creation.py
 rename tests/{test_package.py => test_h5m_in_simulation.py} (59%)

diff --git a/tests/test_h5m_creation.py b/tests/test_h5m_creation.py
new file mode 100644
index 0000000..3c815d7
--- /dev/null
+++ b/tests/test_h5m_creation.py
@@ -0,0 +1,85 @@
+
+# import dagmc_h5m_file_inspector as di
+import cad_to_dagmc
+from vertices_to_h5m import vertices_to_h5m
+import dagmc_h5m_file_inspector as di
+
+"""
+Tests that check that:
+    - h5m files are created
+    - h5m files contain the correct number of volumes
+    - h5m files contain the correct material tags
+
+"""
+
+
+from cadquery import importers
+from OCP.GCPnts import GCPnts_QuasiUniformDeflection
+
+# from cadquery.occ_impl import shapes
+import OCP
+import cadquery as cq
+from OCP.TopLoc import TopLoc_Location
+from OCP.BRep import BRep_Tool
+from OCP.TopAbs import TopAbs_Orientation
+
+
+def test_h5m_production_with_single_volume_list():
+    #     """The simplest geometry, a single 4 sided shape with lists instead of np arrays"""
+
+    stp_files = ["tests/extrude_rectangle.stp", "tests/single_cube.stp"]
+    h5m_files = ["tests/extrude_rectangle.h5m", "tests/single_cube.h5m"]
+
+    for stp_file, h5m_file in zip(stp_files, h5m_files):
+
+        stp_file = cad_to_dagmc.load_stp_file(stp_file)
+
+        merged_stp_file = cad_to_dagmc.merge_surfaces(stp_file)
+        vertices, triangles = cad_to_dagmc.tessellate(merged_stp_file, tolerance=2)
+
+        vertices_to_h5m(
+            vertices=vertices,
+            triangles=[triangles],
+            material_tags=["mat1"],
+            h5m_filename=h5m_file,
+        )
+
+        assert di.get_volumes_and_materials_from_h5m(h5m_file) == {1: 'mat1'}
+
+
+def test_h5m_production_with_multi_volume_list():
+
+    stp_files = [
+        "tests/multi_volume_cylinders.stp",
+        "tests/two_disconnected_cubes.stp",
+        "tests/two_connected_cubes.stp",
+    ]
+    material_tags = [
+        ["mat1", "mat2", "mat3", "mat4", "mat5", "mat6"],
+        ["mat1", "mat2"],
+        ["mat1", "mat2"],
+    ]
+    h5m_files = [
+        "tests/multi_volume_cylinders.h5m",
+        "tests/two_disconnected_cubes.h5m",
+        "tests/two_connected_cubes.h5m",
+    ]
+    for stp_file, mat_tags, h5m_file in zip(stp_files, material_tags, h5m_files):
+
+        stp_file_object = cad_to_dagmc.load_stp_file(stp_file)
+        merged_stp_file = cad_to_dagmc.merge_surfaces(stp_file_object)
+        vertices, triangles = cad_to_dagmc.tessellate_touching_parts(
+            merged_stp_file, tolerance=2
+        )
+
+        vertices_to_h5m(
+            vertices=vertices,
+            triangles=triangles,
+            material_tags=mat_tags,
+            h5m_filename=h5m_file,
+        )
+
+        tags_dict = {}
+        for counter, loop_mat_tag  in enumerate(mat_tags, 1):
+            tags_dict[counter] = loop_mat_tag
+        assert di.get_volumes_and_materials_from_h5m(h5m_file) == tags_dict
diff --git a/tests/test_package.py b/tests/test_h5m_in_simulation.py
similarity index 59%
rename from tests/test_package.py
rename to tests/test_h5m_in_simulation.py
index 01809a4..ffed022 100644
--- a/tests/test_package.py
+++ b/tests/test_h5m_in_simulation.py
@@ -1,33 +1,13 @@
-from vertices_to_h5m import vertices_to_h5m
-from pathlib import Path
-
 # import dagmc_h5m_file_inspector as di
 import openmc
 import openmc_data_downloader as odd
-import math
-import cad_to_dagmc
+
 
 """
-Tests that check that:
-    - h5m files are created
-    - h5m files contain the correct number of volumes
-    - h5m files contain the correct material tags
     - h5m files can be used a transport geometry in DAGMC with OpenMC
 """
 
 
-from cadquery import importers
-from OCP.GCPnts import GCPnts_QuasiUniformDeflection
-
-# from cadquery.occ_impl import shapes
-import OCP
-import cadquery as cq
-from vertices_to_h5m import vertices_to_h5m
-from OCP.TopLoc import TopLoc_Location
-from OCP.BRep import BRep_Tool
-from OCP.TopAbs import TopAbs_Orientation
-
-
 def transport_particles_on_h5m_geometry(
     h5m_filename,
     material_tags,
@@ -111,26 +91,14 @@ def transport_particles_on_h5m_geometry(
 
 
 def test_h5m_production_with_single_volume_list():
-    #     """The simplest geometry, a single 4 sided shape with lists instead of np arrays"""
+    """The simplest geometry, a single 4 sided shape with lists instead of np arrays"""
 
-    stp_files = ["tests/extrude_rectangle.stp", "tests/single_cube.stp"]
-    for stp_file in stp_files:
-        test_h5m_filename = "single_tet.h5m"
+    h5m_files = ["tests/extrude_rectangle.h5m", "tests/single_cube.h5m"]
 
-        stp_file = cad_to_dagmc.load_stp_file(stp_file)
-
-        merged_stp_file = cad_to_dagmc.merge_surfaces(stp_file)
-        vertices, triangles = cad_to_dagmc.tessellate(merged_stp_file, tolerance=2)
-
-        vertices_to_h5m(
-            vertices=vertices,
-            triangles=[triangles],
-            material_tags=["mat1"],
-            h5m_filename=test_h5m_filename,
-        )
+    for h5m_file in h5m_files:
 
         transport_particles_on_h5m_geometry(
-            h5m_filename=test_h5m_filename,
+            h5m_filename=h5m_file,
             material_tags=["mat1"],
         )
 
@@ -148,46 +116,13 @@ def test_h5m_production_with_multi_volume_list():
         ["mat1", "mat2"],
         ["mat1", "mat2"],
     ]
-    for stp_file, mat_tags in zip(stp_files, material_tags):
-
-        stp_file_object = cad_to_dagmc.load_stp_file(stp_file)
-        merged_stp_file = cad_to_dagmc.merge_surfaces(stp_file_object)
-        vertices, triangles = cad_to_dagmc.tessellate_touching_parts(
-            merged_stp_file, tolerance=2
-        )
-
-        vertices_to_h5m(
-            vertices=vertices,
-            triangles=triangles,
-            material_tags=mat_tags,
-            h5m_filename="test.h5m",
-        )
+    h5m_files = [
+        "tests/multi_volume_cylinders.h5m",
+        "tests/two_disconnected_cubes.h5m",
+        "tests/two_connected_cubes.h5m",
+    ]
+    for mat_tags, h5m_file in zip(material_tags, h5m_files):
 
         transport_particles_on_h5m_geometry(
-            h5m_filename="test.h5m", material_tags=mat_tags
+            h5m_filename=h5m_file, material_tags=mat_tags
         )
-
-
-import cad_to_dagmc
-import json
-
-mat_tags = ["mat1", "mat2"]
-# mat_tags=["mat1", "mat2", "mat3", "mat4", "mat5", "mat6"]
-stp_file = cad_to_dagmc.load_stp_file("tests/two_connected_cubes.stp")
-# stp_file = cad_to_dagmc.load_stp_file("tests/multi_volume_cylinders.stp")
-merged_stp_file = cad_to_dagmc.merge_surfaces(stp_file)
-vertices, triangles = cad_to_dagmc.tessellate_touching_parts(
-    merged_stp_file, tolerance=2
-)
-
-with open("data.json", "w") as f:
-    json.dump([vertices, triangles], f, indent=1)
-
-vertices_to_h5m(
-    vertices=vertices,
-    triangles=triangles,
-    material_tags=mat_tags,
-    h5m_filename="test.h5m",
-)
-
-transport_particles_on_h5m_geometry(h5m_filename="test.h5m", material_tags=mat_tags)

From 28a2a4a04cd314642d594c2321f5c44def63f05a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 12:05:42 +0100
Subject: [PATCH 12/17] removed print statement

---
 cad_to_dagmc/core.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/cad_to_dagmc/core.py b/cad_to_dagmc/core.py
index 83c3933..a00900f 100644
--- a/cad_to_dagmc/core.py
+++ b/cad_to_dagmc/core.py
@@ -50,7 +50,7 @@ def merge_surfaces(geometry):
         return solids[0]
 
     for solid in solids:
-        print(type(solid))
+        # print(type(solid))
         # checks if solid is a compound as .val() is not needed for compounds
         if isinstance(solid, (cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid)):
             bldr.AddArgument(solid.wrapped)
@@ -133,7 +133,7 @@ def tessellate_parts(merged_solid, tolerance: float, angularTolerance: float = 0
     loop_counter = 0
 
     for s in merged_solid.Solids():
-        print(s.hashCode())
+        # print(s.hashCode())
         # all_vertices[s.hashCode()] = {}
         triangles_on_solids_faces[s.hashCode()] = {}
         for f in s.Faces():
@@ -213,7 +213,7 @@ def tessellate_touching_parts(
     loop_counter = 0
 
     for s in merged_solid.Solids():
-        print(s.hashCode())
+        # print(s.hashCode())
         # all_vertices[s.hashCode()] = {}
         triangles_on_solids_faces[s.hashCode()] = {}
         for f in s.Faces():
@@ -261,11 +261,11 @@ def tessellate_touching_parts(
                 offset += poly.NbNodes()
 
             else:
-                print("found face in existing faces, reusing triangles")
+                # print("found face in existing faces, reusing triangles")
                 for key_s, value in triangles_on_solids_faces.items():
                     for key_f, face in value.items():
                         if key_f == f.hashCode():
-                            print(f"found face {f.hashCode()}")
+                            # print(f"found face {f.hashCode()}")
                             face_triangles = triangles_on_solids_faces[key_s][key_f]
                             # triangles.append(face_triangles)
                 # triangles_on_solids_faces[s.hashCode()]
@@ -278,14 +278,14 @@ def tessellate_touching_parts(
 
     list_of_triangles_per_solid = []
     for key, value in triangles_on_solids_faces.items():
-        print(key)
+        # print(key)
         triangles_on_solid = []
         for key, face in value.items():
-            print("    ", key, face)
+            # print("    ", key, face)
             triangles_on_solid = triangles_on_solid + face
         list_of_triangles_per_solid.append(triangles_on_solid)
-    for vertice in vertices:
-        print(vertice)
-    print(len(vertices))
+    # for vertice in vertices:
+        # print(vertice)
+    # print(len(vertices))
 
     return vertices, list_of_triangles_per_solid

From 5fa21ddc35876ea1e60937b14bf2de7f1a5e2089 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 12:10:25 +0100
Subject: [PATCH 13/17] added two test blocks

---
 .github/workflows/ci_with_install.yml | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 10e4216..2f9731d 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: install non pypi dependencies
+      - name: install non pypi dependencies for cad creation
         run: |
           apt-get --allow-releaseinfo-change update
           apt-get update -y
@@ -41,11 +41,18 @@ jobs:
           pip install .
           python -c "import cad_to_dagmc"
 
-      - name: Run tests
+      - name: Run cad creation tests
         run: |
           pip install .[tests]
+          pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
+
+      - name: install non pypi dependencies for neutronics
+        run: |
+          mamba uninstall moab
+          mamba uninstall cadquery
           mamba install -c conda-forge -y "openmc=0.13.0=dagmc*nompi*"
-          pytest tests -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
 
-      - name: Upload to codecov
-        uses: codecov/codecov-action@v2
+      - name: Run cad creation tests
+        run: |
+          pip install .[tests]
+          pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml

From 6d3a3c53f4d1f06b71e40a6f3aa9763bdebf4c33 Mon Sep 17 00:00:00 2001
From: shimwell <shimwell@users.noreply.github.com>
Date: Fri, 5 Aug 2022 11:11:11 +0000
Subject: [PATCH 14/17] [skip ci] Apply formatting changes

---
 cad_to_dagmc/core.py       | 2 +-
 tests/test_h5m_creation.py | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/cad_to_dagmc/core.py b/cad_to_dagmc/core.py
index a00900f..f86516f 100644
--- a/cad_to_dagmc/core.py
+++ b/cad_to_dagmc/core.py
@@ -285,7 +285,7 @@ def tessellate_touching_parts(
             triangles_on_solid = triangles_on_solid + face
         list_of_triangles_per_solid.append(triangles_on_solid)
     # for vertice in vertices:
-        # print(vertice)
+    # print(vertice)
     # print(len(vertices))
 
     return vertices, list_of_triangles_per_solid
diff --git a/tests/test_h5m_creation.py b/tests/test_h5m_creation.py
index 3c815d7..3065bea 100644
--- a/tests/test_h5m_creation.py
+++ b/tests/test_h5m_creation.py
@@ -1,4 +1,3 @@
-
 # import dagmc_h5m_file_inspector as di
 import cad_to_dagmc
 from vertices_to_h5m import vertices_to_h5m
@@ -44,7 +43,7 @@ def test_h5m_production_with_single_volume_list():
             h5m_filename=h5m_file,
         )
 
-        assert di.get_volumes_and_materials_from_h5m(h5m_file) == {1: 'mat1'}
+        assert di.get_volumes_and_materials_from_h5m(h5m_file) == {1: "mat1"}
 
 
 def test_h5m_production_with_multi_volume_list():
@@ -80,6 +79,6 @@ def test_h5m_production_with_multi_volume_list():
         )
 
         tags_dict = {}
-        for counter, loop_mat_tag  in enumerate(mat_tags, 1):
+        for counter, loop_mat_tag in enumerate(mat_tags, 1):
             tags_dict[counter] = loop_mat_tag
         assert di.get_volumes_and_materials_from_h5m(h5m_file) == tags_dict

From 14947a81c21ab0d483ea9cb776357156c55c0750 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 12:16:51 +0100
Subject: [PATCH 15/17] removed need for pytest cov

---
 .github/workflows/ci_with_install.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 2f9731d..80b4cbd 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -44,7 +44,8 @@ jobs:
       - name: Run cad creation tests
         run: |
           pip install .[tests]
-          pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
+          pytest tests/test_h5m_creation.py -v
+          # pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
 
       - name: install non pypi dependencies for neutronics
         run: |
@@ -55,4 +56,5 @@ jobs:
       - name: Run cad creation tests
         run: |
           pip install .[tests]
-          pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
+          pytest tests/test_h5m_creation.py -v
+          # pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml

From dddc7d97804a4c4748f1c74f3951f3064de846d5 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 12:23:55 +0100
Subject: [PATCH 16/17] fixed filename typo

---
 .github/workflows/ci_with_install.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 2f9731d..374359c 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -55,4 +55,4 @@ jobs:
       - name: Run cad creation tests
         run: |
           pip install .[tests]
-          pytest tests/test_h5m_creation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
+          pytest tests/test_h5m_in_simulation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml

From 5e3ac0f22ca3ff514b283f46386d3eefb915addf Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 5 Aug 2022 12:28:27 +0100
Subject: [PATCH 17/17] fixed 2nd stage of testing commands

---
 .github/workflows/ci_with_install.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 6f7e3ac..2cb6681 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -53,7 +53,7 @@ jobs:
           mamba uninstall cadquery
           mamba install -c conda-forge -y "openmc=0.13.0=dagmc*nompi*"
 
-      - name: Run cad creation tests
+      - name: Run simulation tests
         run: |
           pip install .[tests]
-          pytest tests/test_h5m_in_simulation.py -v --cov=cad_to_dagmc --cov-append --cov-report term --cov-report xml
+          pytest tests/test_h5m_in_simulation.py -v