Merge dev into main

.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

@@ -7,4 +7,5 @@ docs/build/**
 docs/source/_autosummary/*
 docs/jupyter_execute
 .pytest_cache/**
-build/
+build/
+tests_outputs/

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="jpcatalan@ind.uned.es" },
   { name="Patrick Sauvan", email="psauvan@ind.uned.es" },
@@ -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

src/GEOReverse/Modules/Objects.py

@@ -1,10 +1,13 @@
-from GEOReverse.Modules.buildSolidCell import BuildSolid
-import FreeCAD, Part
-import numpy as np
 import math
-from GEOReverse.Modules.remh import cline
-from GEOReverse.Modules.Utils.booleanFunction import outterTerms,BoolSequence
-from GEOReverse.Modules.Utils.BooleanSolids import buildCTableFromSolids
+
+import FreeCAD
+import numpy as np
+import Part
+
+from .buildSolidCell import BuildSolid
+from .remh import cline
+from .Utils.booleanFunction import BoolSequence, outterTerms
+
 
 class CADCell:
     def __init__(self,stringCell=None):

src/GEOReverse/Modules/Parser/PartialFormatter.py

@@ -1,4 +1,5 @@
 import string
+
 version = '3.6'
 
 def make_label(item):

src/GEOReverse/Modules/Parser/parser.py

@@ -4,10 +4,11 @@
 Functions for parsing MCNP input files.
 """
 
+import os
 import re
 import warnings
-import os
-from GEOReverse.Modules.Parser.PartialFormatter import PartialFormatter
+
+from .PartialFormatter import PartialFormatter
 
 version = '3.6'
 

src/GEOReverse/Modules/Utils/BooleanSolids.py

@@ -2,11 +2,12 @@
 #   Conversion to MCNP v0.0 
 #   Only one solid and planar surfaces
 #
-import FreeCAD
-import BOPTools.SplitAPI
 import math
-import re
-from GEOReverse.Modules.Utils.booleanFunction import BoolSequence
+
+import BOPTools.SplitAPI
+import FreeCAD
+
+from .booleanFunction import BoolSequence
 
 BoolVals = (None,True,False)
 
@@ -481,7 +482,7 @@ def checkSign(solid,surf):
        apex,axis,t,dbl = surf.params
        r = point - apex
        r.normalize()
-       z  = axis.dot(r)
+       z  = round(axis.dot(r),15)
        alpha = math.acos(z)
 
        if alpha > math.atan(t) :

src/GEOReverse/Modules/Utils/booleanFunction.py

@@ -1,4 +1,5 @@
 import re
+
 mostinner=re.compile(r"\([^\(^\)]*\)")                                      # identify most inner parentheses
 number   =re.compile(r"(?P<value>[-+]?\d+)")
 mix      =re.compile(r"(?P<value>([-+]?\d+|\[0+\]))")

src/GEOReverse/Modules/XMLParser.py

@@ -1,4 +1,5 @@
-from GEOReverse.Modules.remh import cline
+from .remh import cline
+
 
 class cellCARD:
 

src/GEOReverse/Modules/XMLinput.py

@@ -1,21 +1,20 @@
+import math
 import os
-import sys
 import re
+import xml.etree.ElementTree as ET
+
 import FreeCAD
-from GEOReverse.Modules.remh import cell_card_string, remove_hash
-from GEOReverse.Modules.Objects import *
-from GEOReverse.Modules.XMLParser import get_cards
-import math
 import numpy as np
 from numpy import linalg as LA
-import xml.etree.ElementTree as ET 
+
+from .Objects import *
+from .XMLParser import get_cards
+
 
 class XMLinput:
     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")
 
         tree = ET.parse(name)
         root = tree.getroot()

src/GEOReverse/Modules/buildCAD.py

@@ -1,9 +1,7 @@
-import FreeCAD, Part
 import BOPTools.SplitAPI
-from GEOReverse.Modules.buildSolidCell import FuseSolid
-from GEOReverse.Modules.Utils.BooleanSolids import buildCTableFromSolids
-from GEOReverse.Modules.Utils.booleanFunction import BoolSequence
 
+from .buildSolidCell import FuseSolid
+from .Utils.booleanFunction import BoolSequence
 
 
 def buildCAD(UnivCell,data,config):

src/GEOReverse/Modules/buildSolidCell.py

@@ -1,12 +1,8 @@
-import FreeCAD, Part
-import BOPTools.SplitAPI
-from   BOPTools import GeneralFuseResult as GFR
-from GEOReverse.Modules.Utils.booleanFunction import BoolSequence
-from GEOReverse.Modules.splitFunction import SplitSolid,splitBase,joinBase
-from GEOReverse.Modules.Utils.BooleanSolids import buildCTableFromSolids
-from GEOReverse.Modules.options import Options
-
-import math
+import Part
+
+from .options import Options
+from .splitFunction import SplitSolid, joinBase, splitBase
+from .Utils.booleanFunction import BoolSequence
 
 
 def getPart(slist):