Merge remote-tracking branch 'upstream/main'

.github/workflows/ci.yml

@@ -0,0 +1,71 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - name: Apt dependencies
+        shell: bash
+        run: |
+          sudo apt -y update
+          sudo apt install -y libgcc-9-dev \
+                              libstdc++-9-dev \
+                              libembree-dev \
+                              python3-dev \
+                              libhdf5-dev \
+                              libeigen3-dev \
+                              cmake
+
+      - name: Python dependencies
+        shell: bash
+        run: |
+          pip3 install numpy \
+                      cython==0.29.37 \
+                      scipy \
+                      matplotlib \
+                      h5py \
+                      pytest \
+                      pytest-cov \
+                      codecov
+
+      - name: Build MOAB
+        shell: bash
+        run: |
+          cd ~
+          git clone https://bitbucket.org/fathomteam/moab.git
+          cd moab
+          git checkout 5.5.1
+          mkdir build
+          cd build
+          cmake -DENABLE_HDF5=ON -DENABLE_BLASLAPACK=OFF -DENABLE_PYMOAB=ON -DCMAKE_INSTALL_PREFIX=$HOME/opt -DCMAKE_BUILD_TYPE=Release ..
+          make -j4
+          make install
+          cd pymoab
+          pip3 install .
+
+      - name: Install
+        shell: bash
+        run: |
+          pip install .
+
+      - name: Test
+        shell: bash
+        run: |
+          pytest -v .
+
+      - name: tmate debug
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3

.gitignore

@@ -1,3 +1,14 @@
-*~
 *.h5m
 __pycache__
+
+# Python distribution
+.settings/
+dist/
+pydagmc.egg-info/
+
+# emacs and vim backups
+*~
+*.swp
+
+# Source build
+build

README.md

@@ -1,6 +1,16 @@
 # PyDAGMC
 
-A convenience interface for examining and reassigning metadata in DAGMC models with PyMOAB.
+PyDAGMC is a Python interface for interacting with DAGMC .h5m files through the embedded topological relationships and metadata contained within. These interactions occur through a set of Python classes corresponding to DAGMC’s metadata Group (a grouping of volumes or surfaces), Volume, and Surface groupings in the mesh database. This interface is intended to provide a simple interface for obtaining information about DAGMC models, replacing significant boilerplate code required to perform the same queries with PyMOAB, the Python interface for MOAB itself.
+
+PyDAGMC classes provide the ability to perform basic queries as properties of the class instances. These queries include:
+
+- number of entities contained within a group
+- volume and surface relationships
+- number of triangles contained underneath any class instance
+- triangle connectivity and coordinates underneath any class instance
+- movement of volumes or surfaces into and out of groups
+- VTK file generation for all triangles contained under any class instance
+
 
 # Example
 
@@ -9,14 +19,20 @@ Code:
 ```python
 import dagmc
 
-groups = dagmc.Group.groups_from_file('dagmc.h5m')
-print(groups)
+model = dagmc.DAGModel('dagmc.h5m')
+
+group_dict = model.groups_by_name
+print(group_dict)
 
 fuel_group = groups['mat:fuel']
 
-v1 = fuel_group.get_volumes()[1]
+v1 = fuel_group.volumes_by_id[1]
 
 print(v1)
+
+new_group = dagmc.Group.create(model, name="my_new_group", group_id=10)
+print(new_group)
+
 ```
 Output:
 
@@ -37,17 +53,19 @@ Volume IDs:
 }
 
 Volume 1, 4092 triangles
+
+Group 10, Name: my_new_group
 ```
 
 Code:
 
 ```python
 # move volume 1 from the fuel group to the group "mat:41"
-groups['mat:fuel'].remove_set(v1)
-groups['mat:41'].add_set(v1)
+group_dict['mat:fuel'].remove_set(v1)
+group_dict['mat:41'].add_set(v1)
 
-print(groups['mat:fuel'])
-print(groups['mat:41'])
+print(group_dict['mat:fuel'])
+print(group_dict['mat:41'])
 ```
 
 Output: