add init_speciate to accelerate the time cost of speciate in the first generation

algorithms/neat/pipeline.py

@@ -32,8 +32,10 @@ class Pipeline:
         self.compile_functions(debug=True)
 
         self.generation = 0
-        self.species_controller.speciate(self.pop_nodes, self.pop_connections,
+        self.species_controller.init_speciate(self.pop_nodes, self.pop_connections)
-                                         self.generation, self.o2o_distance, self.o2m_distance)
+
+        # self.species_controller.speciate(self.pop_nodes, self.pop_connections,
+        #                                  self.generation, self.o2o_distance, self.o2m_distance)
 
         self.best_fitness = float('-inf')
 

algorithms/neat/species.py

@@ -45,6 +45,20 @@ class SpeciesController:
         self.species_idxer = count(0)
         self.species: Dict[int, Species] = {}  # species_id -> species
 
+    def init_speciate(self, pop_nodes: NDArray, pop_connections: NDArray):
+        """
+        speciate for the first generation
+        :param pop_connections:
+        :param pop_nodes:
+        :return:
+        """
+        pop_size = pop_nodes.shape[0]
+        species_id = next(self.species_idxer)
+        s = Species(species_id, 0)
+        members = list(range(pop_size))
+        s.update((pop_nodes[0], pop_connections[0]), members)
+        self.species[species_id] = s
+
     def speciate(self, pop_nodes: NDArray, pop_connections: NDArray, generation: int,
                  o2o_distance: Callable, o2m_distance: Callable) -> None:
         """

examples/xor.py

@@ -23,8 +23,8 @@ def evaluate(forward_func: Callable) -> List[float]:
     return fitnesses.tolist()  # returns a list
 
 
-# @using_cprofile
+@using_cprofile
-@partial(using_cprofile, root_abs_path='/mnt/e/neat-jax/', replace_pattern="/mnt/e/neat-jax/")
+# @partial(using_cprofile, root_abs_path='/mnt/e/neat-jax/', replace_pattern="/mnt/e/neat-jax/")
 def main():
     config = Configer.load_config()
     pipeline = Pipeline(config, seed=11323)