Convert print statements to logging statements

Remove print statements in main.py and library.py that would otherwise print regardless of logging level.

Author: amarkpayne

rmgpy/data/kinetics/library.py

@@ -218,23 +218,23 @@ def convertDuplicatesToMulti(self):
         Merge all marked duplicate reactions in the kinetics library
         into single reactions with multiple kinetics.
         """
-        print "trying to find duplicates"
+        logging.debug("Searching for duplicate reactions...")
         entries_to_remove = []
         for entry0 in self.entries.values():
             if entry0 in entries_to_remove:
                 continue
             reaction0 = entry0.item
             if not reaction0.duplicate:
                 continue
-            print "Found a duplicate reaction: {0}".format(reaction0)
+            logging.debug("Found a duplicate reaction: {0}".format(reaction0))
             duplicates = [entry0]
             for entry in self.entries.values():
                 reaction = entry.item
                 if reaction0 is reaction:
                     continue
                 if reaction0.isIsomorphic(reaction, eitherDirection=False):
                     if reaction0.reversible != reaction.reversible:
-                        print "Reactions isomorphic but with different reversibilities"
+                        logging.debug("Reactions isomorphic but with different reversibilities.")
                         continue
                     duplicates.append(entry)
             if len(duplicates)<=1:
@@ -271,9 +271,9 @@ def convertDuplicatesToMulti(self):
             entry0.longDesc = longDesc
             entries_to_remove.extend(duplicates[1:])
         for entry in entries_to_remove:
-            print "removing duplicate reaction with index {0}.".format(entry.index)
+            logging.debug("Removing duplicate reaction with index {0}.".format(entry.index))
             del(self.entries[entry.index])
-        print "NB. the entries have not been renumbered, so these indices are missing."
+        logging.debug("NB. the entries have not been renumbered, so these indices are missing.")
 
 
     def load(self, path, local_context=None, global_context=None):

rmgpy/rmg/main.py

@@ -1502,9 +1502,9 @@ def initializeLog(verbose, log_file_name):
     if os.path.exists(log_file_name):
         backup = os.path.join(log_file_name[:-7], 'RMG_backup.log')
         if os.path.exists(backup):
-            print "Removing old "+backup
+            logging.info("Removing old "+backup)
             os.remove(backup)
-        print 'Moving {0} to {1}\n'.format(log_file_name, backup)
+        logging.info('Moving {0} to {1}\n'.format(log_file_name, backup))
         shutil.move(log_file_name, backup)
     fh = logging.FileHandler(filename=log_file_name) #, backupCount=3)
     fh.setLevel(min(logging.DEBUG,verbose)) # always at least VERBOSE in the file