fixing prospector complaints

'except Exception': not really nice, but shell scripts will be remove
soon anyway

processing/post/filterTable.py

@@ -21,7 +21,7 @@ def sortingList(labels,whitelistitems):
   names   = []
 
   for label in labels:
-    if re.match('^\d+_',label):
+    if re.match(r'^\d+_',label):
       indices.append(int(label.split('_',1)[0]))
       names.append(label.split('_',1)[1])
     else:
@@ -144,7 +144,7 @@ for name in filenames:
     try:
       table.data_readArray(positions+1)                                                               # read desired columns (indexed 1,...)
       table.data_writeArray()                                                                         # directly write out
-    except:
+    except Exception:
       table.data_rewind()
       atOnce = False                                                                                  # data contains items that prevent array chunking
 

processing/post/groupTable.py

@@ -11,11 +11,12 @@ import damask
 
 
 def periodicAverage(coords, limits):
-  """Centroid in periodic domain, see https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions"""
+  """Centroid in periodic domain, see https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions."""
   theta     = 2.0*np.pi * (coords - limits[0])/(limits[1] - limits[0])
   theta_avg = np.pi + np.arctan2(-np.sin(theta).mean(axis=0), -np.cos(theta).mean(axis=0))
   return limits[0] + theta_avg * (limits[1] - limits[0])/2.0/np.pi
 
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -73,7 +74,7 @@ try:
                         globals().get(funcModule) or
                         __import__(funcModule), 
                         funcName)
-except:
+except Exception:
   mapFunction = None
 
 if options.label is []:

processing/pre/seeds_fromRandom.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 # ------------------------------------------ aux functions ---------------------------------
 
 def kdtree_search(cloud, queryPoints):
-  """Find distances to nearest neighbor among cloud (N,d) for each of the queryPoints (n,d)"""
+  """Find distances to nearest neighbor among cloud (N,d) for each of the queryPoints (n,d)."""
   n = queryPoints.shape[0]
   distances = np.zeros(n,dtype=float)
   tree = spatial.cKDTree(cloud)
@@ -23,7 +23,8 @@ def kdtree_search(cloud, queryPoints):
     distances[i], index = tree.query(queryPoints[i])
 
   return distances
-    
+
+
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------