Merge pull request #14 from fusion-energy/develop

Only adding mat: prefix if not already present

.github/workflows/anaconda-publish.yml

@@ -8,15 +8,15 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    # This container includes libgl1-mesa-glx, anaconda-client and conda-build
-    # https://github.com/shimwell/miniconda3_docker_image/blob/main/Dockerfile
-    container: ghcr.io/shimwell/miniconda
+    container: continuumio/miniconda3:4.10.3
 
     steps:
       - uses: actions/checkout@v2
 
       - name: Set up conda
         run: |
+            apt-get --allow-releaseinfo-change update
+            conda install -y anaconda-client conda-build
             conda config --set anaconda_upload no
       - name: Build and publish to conda
         env:

.github/workflows/ci_with_install.yml

@@ -23,6 +23,11 @@ jobs:
       - name: install package
         run: |
           conda install -c conda-forge moab
+          pip install .
+          python -c "import stl_to_h5m"
+
+      - name: install package with tests
+        run: |
           pip install .[tests]
 
       - name: Run test_utils

.github/workflows/conda-build-test.yml

@@ -0,0 +1,27 @@
+name: conda-build-test
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - develop
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: continuumio/miniconda3:4.10.3
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up conda
+        run: |
+            apt-get --allow-releaseinfo-change update
+            conda install -y anaconda-client conda-build
+            conda config --set anaconda_upload no
+      - name: Build and test
+        env:
+          GIT_DESCRIBE_TAG: 0.1
+        run: |
+            conda build conda -c fusion-energy -c conda-forge --config-file conda/conda_build_config.yaml

README.md

@@ -6,7 +6,8 @@
 [![Upload Python Package](https://github.com/fusion-energy/stl_to_h5m/actions/workflows/python-publish.yml/badge.svg)](https://github.com/fusion-energy/stl_to_h5m/actions/workflows/python-publish.yml)
 [![anaconda-publish](https://github.com/fusion-energy/stl_to_h5m/actions/workflows/anaconda-publish.yml/badge.svg)](https://github.com/fusion-energy/stl_to_h5m/actions/workflows/anaconda-publish.yml)
 
-
+[![conda-publish](https://anaconda.org/fusion-energy/stl_to_h5m/badges/version.svg)](https://anaconda.org/fusion-energy/stl_to_h5m)
+[![PyPI](https://img.shields.io/pypi/v/stl-to-h5m?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/stl_to_h5m/)
 
 This is a minimal Python package that provides a Python API interfaces for converting multiple STL files into a DAGMC h5m file ready for use in simulation.
 
@@ -15,18 +16,20 @@ Convert STL files to a DAGMC h5m file complete with material tags and ready for
 **warning** this approach does not imprint and merge the geometry and therefore
 requires that the STL files do not overlap. Overlaps could lead to particles
 being lost during transport. If imprinting and merging is required consider
-using [cad-to-h5m](https://github.com/fusion-energy/cad_to_h5m).
+using [Paramak export_dagmc_h5m()](https://paramak.readthedocs.io/en/main/)
+method or [cad-to-h5m](https://github.com/fusion-energy/cad_to_h5m) to make the
+DAGMC geometry.
 
 It is strongly advised to used the DAGMC overlap checker to check the
-resulting h5m file (see checking for overlaps secton below).
+resulting h5m file (see checking for overlaps section below).
 
 
 # Installation - Conda
 
 This single line command should install the package and dependencies (including moab)
 
 ```bash
-conda install -c fusion-energy -c conda-forge stl_to_h5m
+conda install -c fusion-energy -c fusion-energy stl_to_h5m
 ```
 
 # Installation - Pip + Conda

conda/conda_build_config.yaml

@@ -3,5 +3,3 @@ python:
     - 3.9
     - 3.8
     - 3.7
-moab:
-    - 5.3.1

setup.cfg

@@ -27,7 +27,8 @@ packages = find:
 python_requires= >=3.6
 install_requires=
     numpy >= 1.21.1
-    # moab is required as well but installed via conda
+    # moab is required as well but not available on pypi
+    # moab can be installed via conda
 
 [options.extras_require]
 tests = 

stl_to_h5m/core.py

@@ -171,7 +171,10 @@ def _add_stl_to_moab_core(
 
     # reflective is a special case that should not have mat: in front
     if not material_name == "reflective":
-        dag_material_tag = "mat:{}".format(material_name)
+        if material_name.startswith("mat:"):
+            dag_material_tag = material_name
+        else:
+            dag_material_tag = "mat:{}".format(material_name)
     else:
         dag_material_tag = material_name
 

tests/test_python_api.py

@@ -1,7 +1,5 @@
 import os
-import tarfile
 import unittest
-import urllib.request
 from pathlib import Path
 
 from stl_to_h5m import stl_to_h5m
@@ -68,3 +66,21 @@ def test_h5m_file_creation_and_contents_from_multiple_h5m_files(self):
             1: "mat1",
             2: "mat2",
         }
+
+    def test_tagnames_in_h5m_file(self):
+        """Checks that a h5m file is created with the correct tag names"""
+
+        test_h5m_filename = "test_dagmc.h5m"
+        os.system(f"rm {test_h5m_filename}")
+
+        returned_filename = stl_to_h5m(
+            files_with_tags=[("tests/part2.stl", "mat:mat1")],
+            h5m_filename=test_h5m_filename,
+        )
+
+        assert Path(test_h5m_filename).is_file()
+        assert Path(returned_filename).is_file()
+        assert test_h5m_filename == returned_filename
+        assert di.get_volumes_from_h5m(test_h5m_filename) == [1]
+        assert di.get_materials_from_h5m(test_h5m_filename) == ["mat1"]
+        assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {1: "mat1"}