refactor genome.py use (C, 4) to replace (2, N, N) to represent connections

faster, faster and faster!

examples/function_tests.py

@@ -0,0 +1,49 @@
+import jax
+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.genome.crossover import crossover
+
+
+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])
+    key = jax.random.PRNGKey(0)
+    new_node_idx = 100
+    while True:
+        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 idx, (zn1, zc1, zn2, zc2) in enumerate(zip(n1, c1, n2, c2)):
+        #     n, c = crossover(crossover_keys[idx], zn1, zc1, zn2, zc2)
+        #     try:
+        #         check_array_valid(n, c, input_idx, output_idx)
+        #     except AssertionError as e:
+        #         crossover(crossover_keys[idx], zn1, zc1, zn2, zc2)
+
+        pop_nodes, pop_connections = crossover_func(crossover_keys, n1, c1, n2, c2)
+
+        for i in range(len(pop_nodes)):
+            check_array_valid(pop_nodes[i], pop_connections[i], input_idx, output_idx)
+
+        print(new_node_idx)
+
+