Replace misc print statements with logging or exceptions

Author: mliu49

rmgpy/__init__.py

@@ -65,7 +65,7 @@ def __setitem__(self, key, value):
         elif key == 'test_data.directory':
             value = os.path.abspath(os.path.expandvars(value))
         else:
-            print('Unexpecting setting "{0}" encountered.'.format(key))
+            raise SettingsError('Unexpecting setting "{0}" encountered.'.format(key))
         self.sources[key] = '-'
         super(Settings, self).__setitem__(key, value)
 

rmgpy/cantherm/gaussian.py

@@ -157,7 +157,7 @@ def loadGeometry(self):
             elif number[i] == 17:
                 mass[i] = 35.4527
             else:
-                print 'Atomic number {0:d} not yet supported in loadGeometry().'.format(number[i])
+                raise NotImplementedError('Atomic number {0:d} not yet supported in loadGeometry().'.format(number[i]))
 
         return coord, number, mass
 

rmgpy/cantherm/qchem.py

@@ -175,7 +175,7 @@ def loadGeometry(self):
                 mass[i] = 35.4527
                 number.append('17')
             else:
-                print 'Atomic atom {0:d} not yet supported in loadGeometry().'.format(atom[i])
+                raise NotImplementedError('Atomic atom {0:d} not yet supported in loadGeometry().'.format(atom[i]))
         number = numpy.array(number, numpy.int)       
         return coord, number, mass
 

rmgpy/data/kinetics/family.py

@@ -944,8 +944,8 @@ def generateProductTemplate(self, reactants0):
                     try:
                         if s.isIdentical(struct): break
                     except KeyError:
-                        print struct.toAdjacencyList()
-                        print s.toAdjacencyList()
+                        logging.error(struct.toAdjacencyList())
+                        logging.error(s.toAdjacencyList())
                         raise
                 else:
                     productStructureList[i].append(struct)

rmgpy/species.py

@@ -274,9 +274,9 @@ def toCantera(self, useChemkinIdentifier = False):
         if self.thermo:
             try:
                 ctSpecies.thermo = self.thermo.toCantera()
-            except Exception, e:
-                print e
-                raise Exception('Could not convert thermo to create Cantera Species object. Check that thermo is a NASA polynomial.')
+            except Exception:
+                logging.error('Could not convert thermo to create Cantera Species object. Check that thermo is a NASA polynomial.')
+                raise
 
         if self.transportData:
             ctSpecies.transport = self.transportData.toCantera()