Remove naturally extinct species from stagnation tracking.

Fixed incorrect species fitness tracking.

Author: CodeReclaimers

neat/reproduction.py

@@ -2,7 +2,7 @@
 import random
 
 from neat.indexer import Indexer
-from neat.six_util import iteritems, itervalues
+from neat.six_util import iteritems, iterkeys, itervalues
 
 # TODO: Provide some sort of optional cross-species performance criteria, which
 # are then used to control stagnation and possibly the mutation rate configuration.
@@ -52,8 +52,8 @@ def create_new(self, genome_type, genome_config, num_genomes):
         return new_genomes
 
     def reproduce(self, config, species, pop_size):
-        # TODO: I don't like this modification of the species object,
-        # because it requires internal knowledge of the object.
+        # TODO: I don't like this modification of the species and stagnation objects,
+        # because it requires internal knowledge of the objects.
 
         # Filter out stagnated species and collect the set of non-stagnated species members.
         num_remaining = 0
@@ -148,6 +148,11 @@ def reproduce(self, config, species, pop_size):
                 new_population[gid] = child
                 self.ancestors[gid] = (parent1_id, parent2_id)
 
+        # Remove empty species from the stagnation tracking.
+        keys = list(iterkeys(self.stagnation.stagnant_counts))
+        for sid in keys:
+            if sid not in species.species:
+                self.stagnation.remove(sid)
 
         # Sort species by ID (purely for ease of reading the reported list).
         # TODO: This should probably be done by the species object.

neat/stagnation.py

@@ -10,7 +10,7 @@ class DefaultStagnation(object):
     @classmethod
     def parse_config(cls, param_dict):
         config = {'species_fitness_func': 'mean',
-                       'max_stagnation': 15}
+                  'max_stagnation': 15}
         config.update(param_dict)
 
         return config
@@ -53,10 +53,10 @@ def update(self, species):
             prev_fitness = self.previous_fitnesses.get(sid, -sys.float_info.max)
             if fitness > prev_fitness:
                 scount = 0
+                self.previous_fitnesses[sid] = fitness
             else:
                 scount = self.stagnant_counts.get(sid, 0) + 1
 
-            self.previous_fitnesses[sid] = fitness
             self.stagnant_counts[sid] = scount
 
             is_stagnant = scount >= self.max_stagnation