Fix format specifier when logging species pruning.

Hopefully this closes #2043

The Species class doesn't have an ability to interpret a format
specifier "<56" (although the Species.label would, because it's a string.

Anyway, while fixing that I also changed some other 
logging.debug() statements over to the old-fashioned format syntax
and left the formatting to the logging module. This way, it formats 
the string "lazily", and if you're not running in verbose mode (i.e.
the debug messages aren't going to be printed anyway) then it doesn't
bother doing the formatting. Might save a few nanoseconds :-)

Because we almost always run with logging.info() showing, I left those alone.

Author: rwest

rmgpy/rmg/model.py

@@ -304,7 +304,7 @@ def make_new_species(self, object, label='', reactive=True, check_existing=True,
         # This may change later after getting thermo in self.generate_thermo()
         if not spec.label:
             spec.label = spec.smiles
-        logging.debug('Creating new species {0}'.format(spec.label))
+        logging.debug('Creating new species %s', spec.label)
 
         formula = molecule.get_formula()
         if formula in self.species_dict:
@@ -452,11 +452,11 @@ def make_new_reaction(self, forward, check_existing=True, generate_thermo=True):
 
         # Note in the log
         if isinstance(forward, TemplateReaction):
-            logging.debug('Creating new {0} template reaction {1}'.format(forward.family, forward))
+            logging.debug('Creating new %s template reaction %s', forward.family, forward)
         elif isinstance(forward, DepositoryReaction):
-            logging.debug('Creating new {0} reaction {1}'.format(forward.get_source(), forward))
+            logging.debug('Creating new %s reaction %s', forward.get_source(), forward)
         elif isinstance(forward, LibraryReaction):
-            logging.debug('Creating new library reaction {0}'.format(forward))
+            logging.debug('Creating new library reaction %s', forward)
         else:
             raise Exception("Unrecognized reaction type {0!s}".format(forward.__class__))
 
@@ -1044,7 +1044,7 @@ def add_species_to_core(self, spec):
         if spec in self.edge.species:
 
             # If species was in edge, remove it
-            logging.debug("Removing species {0} from edge.".format(spec))
+            logging.debug("Removing species %s from edge.", spec)
             self.edge.species.remove(spec)
 
             # Search edge for reactions that now contain only core species;
@@ -1063,7 +1063,7 @@ def add_species_to_core(self, spec):
             # Move any identified reactions to the core
             for rxn in rxn_list:
                 self.add_reaction_to_core(rxn)
-                logging.debug("Moving reaction from edge to core: {0}".format(rxn))
+                logging.debug("Moving reaction from edge to core: %s", rxn)
         return rxn_list
 
     def add_species_to_edge(self, spec):
@@ -1123,7 +1123,7 @@ def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_
         """
         Tmax = self.Tmax
         num_to_remove = len(self.edge.species) - maximum_edge_species
-        logging.debug('Planning to remove {0} species'.format(num_to_remove))
+        logging.debug('Planning to remove %d species', num_to_remove)
         iteration = self.iteration_num
 
         if num_to_remove > 0:  # implies flux pruning is off or did not trigger
@@ -1149,7 +1149,7 @@ def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_
                     num_to_remove -= 1
                 ind += 1
 
-            logging.debug('found {0} eligible species for filtering'.format(len(remove_spcs)))
+            logging.debug('Found %d eligible species for filtering', len(remove_spcs))
 
             for i, spc in enumerate(remove_spcs):
                 logging.info('Removing species {0} from edge to meet maximum number of edge species, Gibbs '
@@ -1176,7 +1176,7 @@ def remove_empty_pdep_networks(self):
         if len(networks_to_delete) > 0:
             logging.info('Deleting {0:d} empty pressure-dependent reaction networks'.format(len(networks_to_delete)))
             for network in networks_to_delete:
-                logging.debug('    Deleting empty pressure dependent reaction network #{0:d}'.format(network.index))
+                logging.debug('    Deleting empty pressure dependent reaction network #%d', network.index)
                 source = tuple(network.source)
                 nets_with_this_source = self.network_dict[source]
                 nets_with_this_source.remove(network)
@@ -1255,17 +1255,18 @@ def prune(self, reaction_systems, tol_keep_in_edge, tol_move_to_core, maximum_ed
 
         # Actually do the pruning
         if prune_due_to_rate_counter > 0:
-            logging.info('Pruning {0:d} species whose rate ratios against characteristic rate did not exceed the '
-                         'minimum threshold of {1:g}'.format(prune_due_to_rate_counter, tol_keep_in_edge))
+            logging.info('Pruning %d species whose rate ratios against characteristic rate did not exceed the '
+                         'minimum threshold of %g', prune_due_to_rate_counter, tol_keep_in_edge)
             for index, spec in species_to_prune[0:prune_due_to_rate_counter]:
-                logging.info('Pruning species {0:<56}'.format(spec))
-                logging.debug('    {0:<56}    {1:10.4e}'.format(spec, max_edge_species_rate_ratios[index]))
+                logging.info('Pruning species %s', spec)
+                logging.debug('    %-56s    %10.4e', spec, max_edge_species_rate_ratios[index])
                 self.remove_species_from_edge(reaction_systems, spec)
         if len(species_to_prune) - prune_due_to_rate_counter > 0:
-            logging.info('Pruning {0:d} species to obtain an edge size of {1:d} species'.format(len(species_to_prune) - prune_due_to_rate_counter, maximum_edge_species))
+            logging.info('Pruning %d species to obtain an edge size of %d species',
+                         len(species_to_prune) - prune_due_to_rate_counter, maximum_edge_species)
             for index, spec in species_to_prune[prune_due_to_rate_counter:]:
-                logging.info('Pruning species {0:<56}'.format(spec))
-                logging.debug('    {0:<56}    {1:10.4e}'.format(spec, max_edge_species_rate_ratios[index]))
+                logging.info('Pruning species %s', spec)
+                logging.debug('    %-56s    %10.4e', spec, max_edge_species_rate_ratios[index])
                 self.remove_species_from_edge(reaction_systems, spec)
 
         # Delete any networks that became empty as a result of pruning