finish jit-able speciate function

next time i'll create a new branch

examples/jitable_speciate_t.py

@@ -0,0 +1,67 @@
+import jax
+import jax.numpy as jnp
+import numpy as np
+from algorithms.neat.function_factory import FunctionFactory
+from algorithms.neat.genome.debug.tools import check_array_valid
+from utils import Configer
+from algorithms.neat.jitable_speciate import jitable_speciate
+from algorithms.neat.genome.crossover import crossover
+from algorithms.neat.genome.utils import I_INT
+from time import time
+
+if __name__ == '__main__':
+    config = Configer.load_config()
+    function_factory = FunctionFactory(config, debug=True)
+    initialize_func = function_factory.create_initialize()
+
+    pop_nodes, pop_connections, input_idx, output_idx = initialize_func()
+    mutate_func = function_factory.create_mutate(pop_nodes.shape[1], pop_connections.shape[1])
+    crossover_func = function_factory.create_crossover(pop_nodes.shape[1], pop_connections.shape[1])
+
+    N, C, species_size = function_factory.init_N, function_factory.init_C, 20
+    spe_center_nodes = np.full((species_size, N, 5), np.nan)
+    spe_center_connections = np.full((species_size, C, 4), np.nan)
+    spe_center_nodes[0] = pop_nodes[0]
+    spe_center_connections[0] = pop_connections[0]
+
+    key = jax.random.PRNGKey(0)
+    new_node_idx = 100
+
+    while True:
+        start_time = time()
+        key, subkey = jax.random.split(key)
+        mutate_keys = jax.random.split(subkey, len(pop_nodes))
+        new_nodes = np.arange(new_node_idx, new_node_idx + len(pop_nodes))
+        new_node_idx += len(pop_nodes)
+        pop_nodes, pop_connections = mutate_func(mutate_keys, pop_nodes, pop_connections, new_nodes)
+        pop_nodes, pop_connections = jax.device_get([pop_nodes, pop_connections])
+        # for i in range(len(pop_nodes)):
+        #     check_array_valid(pop_nodes[i], pop_connections[i], input_idx, output_idx)
+        idx1 = np.random.permutation(len(pop_nodes))
+        idx2 = np.random.permutation(len(pop_nodes))
+
+        n1, c1 = pop_nodes[idx1], pop_connections[idx1]
+        n2, c2 = pop_nodes[idx2], pop_connections[idx2]
+        crossover_keys = jax.random.split(subkey, len(pop_nodes))
+
+        # for i in range(len(pop_nodes)):
+        #     check_array_valid(pop_nodes[i], pop_connections[i], input_idx, output_idx)
+
+        #speciate next generation
+
+        idx2specie, spe_center_nodes, spe_center_cons = jitable_speciate(pop_nodes, pop_connections, spe_center_nodes, spe_center_connections,
+                               compatibility_threshold=2.5)
+
+        idx2specie = np.array(idx2specie)
+        spe_dict = {}
+        for i in range(len(idx2specie)):
+            spe_idx = idx2specie[i]
+            if spe_idx not in spe_dict:
+                spe_dict[spe_idx] = 1
+            else:
+                spe_dict[spe_idx] += 1
+
+        print(spe_dict)
+        assert np.all(idx2specie != I_INT)
+        print(time() - start_time)
+        # print(idx2specie)