Merge dev into main (#67)

* update Fuzzy write function

* several stp file update

* script to color CAD document following material label

* fix rounding error of z value acos(z) evaluation

* Add a bug report template and .gitignore (#44)

* Removed unused imports and variables (#35)

* raise value error instead of exit (#41)

* Update to testing path (#40)

* changed hardcoded path to work for all users

* path update

* Update bug_report.md

* raising catchable error instead of exit (#47)

* raising catchable error instead of exit

* added new line

* added try for freecad import (#48)

* Solve SyntaxtError producing a bug (#49)

* Solve SyntaxtError producing a bug

* Limit the amount of decimals printed in the enclosure comment

* fixed error units in OpenMC output

* GEOUNED training presentation added (#53)

* Adding minimal ci to check cad converts (#52)

* added minimal CI

* all step files

* added ci yml

* removed freecadcmd arg

* Update pyproject.toml

Update url links to "GEOUNED-org"

* typo correction to test if CI is working (#54)

* typo correction

* [skip ci] added ci status badge

* opening up ci to all os systems

* fix small bug with torus (bad identification of closed mozaic faces)

* Adding minimal volume checking CI comparing CAD and CSG volumes (#56)

* added volume test to ci

* removed if os cond

* added csg vs cad volume for **most** stp files

* Added mkdocs (#57)

* added example docs

* added docs deps

* Reverting mkdocs PR 57 (#58)

* Revert "added example docs"

This reverts commit bd1c67a.

* Revert "added docs deps"

This reverts commit f31d241.

* Adding minimal particle transport tests on resulting csg files (#59)

* added transport tests

* removed files that break, raised issue

* [skip ci] remove prints

* added link to issue

* Add the name to the cells in OpenMC to improve identification (#61)

The name is the same that is used in MCNP inputs cell.Comments

* converting with no simplification = more geometry works (#62)

* reduced number of skiped geoms (#63)

* [skip ci] corrected bade to main branch (#64)

* Improved import statements (#65)

* changed single file from package to relative imports

* 2nd file converted to relative imports

* converted more fiels to relative import

* relative imports everywhere

* isort on all imports

* Add bug report and .gitignore to main (#45) (#66)

Co-authored-by: AlvaroCubi <[email protected]>

* added standard gitignore for python project (#68)

---------

Co-authored-by: psauvan <[email protected]>
Co-authored-by: Tony <[email protected]>
Co-authored-by: Jonathan Shimwell <[email protected]>
Co-authored-by: Aljaz Kolsek (F4E) <[email protected]>
Co-authored-by: Emilio Castro <[email protected]>

.github/workflows/ci.yml

@@ -0,0 +1,62 @@
+name: CI testing
+
+on:
+    pull_request:
+      branches:
+        - dev
+        - main
+    push:
+      branches:
+        - main
+
+jobs:
+    testing:
+      name: CI (Python=${{ matrix.python-version }}, OS=${{ matrix.os }})
+      runs-on: ${{ matrix.os }}
+      defaults:
+        run:
+          shell: bash -el {0}
+      strategy:
+        matrix:
+          os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+          python-version: ["3.11"]
+
+          include:
+            - python-version: "3.8"
+              os: "ubuntu-latest"
+            - python-version: "3.9"
+              os: "ubuntu-latest"
+            - python-version: "3.10"
+              os: "ubuntu-latest"
+      steps:
+        - name: checkout actions
+          uses: actions/checkout@v4
+        - uses: conda-incubator/setup-miniconda@v3
+          with:
+            auto-update-conda: true
+            python-version: ${{ matrix.python-version }}
+            channels: conda-forge
+
+        - name: install dependencies
+          run: conda install -c conda-forge freecad -y
+
+        - name: install package
+          run: |
+            python -m pip install --upgrade pip
+            python -m pip install .
+            python -c 'import GEOUNED'
+            python -c 'from GEOReverse import reverse'
+            python -m pip install .[tests]
+
+        - name: testing GEOUNED functionality
+          run: python -m pytest -v tests/test_convert.py
+
+        - name: install openmc
+          if: ${{ matrix.os == 'ubuntu-latest'}}
+          run: conda install -c conda-forge openmc -y
+
+        - name: testing with OpenMC
+          if: ${{ matrix.os == 'ubuntu-latest'}}
+          run: |
+            python -m pytest -v tests/test_volumes.py
+            python -m pytest -v tests/test_transport.py

.gitignore

@@ -1,10 +1,174 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# openmc output files
+*.h5
+*.xml
+
+# testing folder
+tests_outputs/
+
 .vscode
 **/__pycache__
-.coverage
-htmlcov/*
 docs/source/_build/**
 docs/build/**
 docs/source/_autosummary/*
 docs/jupyter_execute
-.pytest_cache/**
-build/

README.md

@@ -1,3 +1,5 @@
+[![CI testing](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/ci.yml)
+
 # GEOUNED
 A tool to convert from CAD to CSG & CSG to CAD for Monte Carlo transport codes (MCNP & OpenMC).
 This repository contains the implementation of the algorithm presented in the paper [GEOUNED: A new conversion tool from CAD to Monte Carlo geometry](https://doi.org/10.1016/j.net.2024.01.052).
@@ -27,7 +29,7 @@ In that case you can install directly de module using:
 C:\Program Files\FreeCAD 0.XX\bin\python.exe -m pip install git+https://github.com/GEOUNED-code/GEOUNED.git
 ```
 using this option you have directly access to both FreeCAD and GEOUNED python modules. 
-Furthermore, using this python compabilities problems between different versions of python are avoided (some dynamic libraries of FreeCAD depends on the version of python used during the built process). 
+Furthermore, using this python compatibilities problems between different versions of python are avoided (some dynamic libraries of FreeCAD depends on the version of python used during the built process). 
 
 ## How to use
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "GEOUNED"
-version = "1.0.0"
+version = "1.0.1"
 authors = [
   { name="Juan-Pablo Catalan", email="[email protected]" },
   { name="Patrick Sauvan", email="[email protected]" },
@@ -22,6 +22,11 @@ classifiers = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/GEOUNED-code"
-Repository = "https://github.com/GEOUNED-code/GEOUNED"
-Documentation = "https://github.com/GEOUNED-code/GEOUNED/docs"
+Homepage = "https://github.com/GEOUNED-org"
+Repository = "https://github.com/GEOUNED-org/GEOUNED"
+Documentation = "https://github.com/GEOUNED-org/GEOUNED/docs"
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+]

scripts/colorCADmat.py

@@ -0,0 +1,50 @@
+import re
+import sys
+
+sys.path.append('/usr/lib64/freecad/lib64/')
+import ImportGui
+
+bd = 255
+gd = 255*255
+rd = 255* 255* 255
+matNumber=re.compile(r"Material_(?P<matnum>\d+)") 
+
+def getColor(num,vmin=0,vmax=rd):
+    colRange = rd
+    dnum = vmax - vmin 
+    dx = num - vmin
+    scale = colRange/dnum 
+    snum = dx * scale + 1
+
+    red = snum//gd
+    r  = snum - red * gd
+    green = r // bd
+    blue = r - green * bd
+    return (red/255,green/255,blue/255)
+
+def setColorMaterial(documents):
+    featureObj = []
+    matMin = 999999999
+    matMax = 0
+    for obj in documents.Objects:
+       if obj.TypeId == 'Part::Feature' :
+              for o in obj.InListRecursive:
+                   m = matNumber.search(o.Label)
+                   if m :
+                         mat = int(m.group('matnum'))
+                         matMin = min(matMin,mat)
+                         matMax = max(matMax,mat)
+                         featureObj.append((obj,mat))
+
+    for  obj,mat in featureObj: 
+           obj.ViewObject.ShapeColor = getColor(mat,matMin,matMax)   
+
+
+# color solids in a Freecad document with respect to the material number
+doc = App.ActiveDocument
+setColorMaterial(doc)
+name = doc.Label
+outname = name+'_color'
+ImportGui.export(doc.RootObjects,outname+'.stp')
+doc.saveAs(outname+'.FCStd')
+

scripts/geouned

@@ -32,11 +32,9 @@ elif len(sys.argv) == 3:
       runReverse = True
       inifile = sys.argv[1]
    else:
-      print('Bad option')
-      exit()
+      raise ValueError('Bad option')
 else:
-   print('Too many input arguments')
-   exit()
+   raise ValueError('Too many input arguments')
 
 
 if not runReverse :

scripts/geouned.py

@@ -31,12 +31,10 @@
       runReverse = True
       inifile = sys.argv[1]
    else:
-      print('Bad option')
-      exit()
-else:
-   print('Too many input arguments')
-   exit()
+      raise ValueError('Bad option')
 
+else:
+   raise ValueError('Too many input arguments')
 
 if not runReverse :
   GEO = GEOUNED.GEOUNED(inifile)

src/GEOReverse/Modules/MCNPinput.py

@@ -1,20 +1,20 @@
+import math
 import os
-import sys
 import re
+
 import FreeCAD
-from GEOReverse.Modules.Parser import parser  as mp
-from GEOReverse.Modules.remh import cell_card_string, remove_hash
-from GEOReverse.Modules.Objects import *
-import math
 import numpy as np
 from numpy import linalg as LA
 
+from .Objects import *
+from .Parser import parser as mp
+from .remh import cell_card_string, remove_hash
+
+
 class MCNPinput:
     def __init__(self,name):
         if not os.path.isfile(name):
-            print("File %s does not exist" %name)
-            sys.exit()
-            return
+            raise FileNotFoundError (f"File {name} does not exist")
         self.__inputcards__  = list(mp.get_cards(name))
         self.Transformations = self.__getTransList__()
         return