pack causes trouble with tests ..

processing/pre/geom_addPrimitive.py

@@ -132,7 +132,4 @@ for name in filenames:
   damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_canvas.py

@@ -61,7 +61,7 @@ for name in filenames:
   canvas = np.full(new,options.fill if options.fill is not None
                   else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
 
-  l = np.clip( offset,    0,np.minimum(old  +offset,new))
+  l = np.clip( offset,    0,np.minimum(old  +offset,new))                                           # noqa
   r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
   L = np.clip(-offset,    0,np.minimum(new  -offset,old))
   R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
@@ -71,4 +71,4 @@ for name in filenames:
   damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_clean.py

@@ -39,4 +39,4 @@ for name in filenames:
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
   damask.util.croak(geom.clean(options.stencil))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_fromDREAM3D.py

@@ -155,4 +155,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  geom.to_file(os.path.splitext(name)[0]+'.geom')
+  geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False)

processing/pre/geom_fromMinimalSurface.py

@@ -89,7 +89,4 @@ geom=damask.Geom(microstructure,options.size,
                  comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromOsteonGeometry.py

@@ -145,7 +145,4 @@ geom = damask.Geom(microstructure.reshape(grid),
                    homogenization=options.homogenization,comments=header)
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromScratch.py

@@ -63,7 +63,4 @@ geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype)
                    comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromTable.py

@@ -152,7 +152,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_fromVoronoiTessellation.py

@@ -302,7 +302,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_grainGrowth.py

@@ -172,7 +172,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_mirror.py

@@ -44,4 +44,4 @@ for name in filenames:
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
   damask.util.croak(geom.mirror(options.directions,options.reflect))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_renumber.py

@@ -34,4 +34,4 @@ for name in filenames:
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
   damask.util.croak(self.renumber)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_rescale.py

@@ -58,4 +58,4 @@ for name in filenames:
   geom.scale(new_grid)
   damask.util.croak(geom.update(microstructure = None,size = new_size))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_rotate.py

@@ -95,4 +95,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_translate.py

@@ -58,7 +58,4 @@ for name in filenames:
   damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_vicinityOffset.py

@@ -82,4 +82,4 @@ for name in filenames:
                                            geom.microstructure + offset,geom.microstructure)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  geom.to_file(sys.stdout if name is None else name)
+  geom.to_file(sys.stdout if name is None else name,pack=False)

python/damask/geom.py

@@ -519,5 +519,5 @@ class Geom():
         for i, oldID in enumerate(np.unique(self.microstructure)):
           renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
 
-        return self.update(renumbered))
+        return self.update(renumbered)
         #self.add_comments('tbd')