change repo structure; modify readme

examples/func_fit/xor3d_hyperneat.py

@@ -1,51 +0,0 @@
-from pipeline import Pipeline
-from algorithm.neat import *
-from algorithm.hyperneat import *
-from utils import Act
-
-from problem.func_fit import XOR3d
-
-if __name__ == '__main__':
-    pipeline = Pipeline(
-        algorithm=HyperNEAT(
-            substrate=FullSubstrate(
-                input_coors=[(-1, -1), (0.333, -1), (-0.333, -1), (1, -1)],
-                hidden_coors=[
-                    (-1, -0.5), (0.333, -0.5), (-0.333, -0.5), (1, -0.5),
-                    (-1, 0), (0.333, 0), (-0.333, 0), (1, 0),
-                    (-1, 0.5), (0.333, 0.5), (-0.333, 0.5), (1, 0.5),
-                ],
-                output_coors=[(0, 1), ],
-            ),
-            neat=NEAT(
-                species=DefaultSpecies(
-                    genome=DefaultGenome(
-                        num_inputs=4,  # [-1, -1, -1, 0]
-                        num_outputs=1,
-                        max_nodes=50,
-                        max_conns=100,
-                        node_gene=DefaultNodeGene(
-                            activation_default=Act.tanh,
-                            activation_options=(Act.tanh,),
-                        ),
-                    ),
-                    pop_size=10000,
-                    species_size=10,
-                    compatibility_threshold=3.5,
-                ),
-            ),
-            activation=Act.sigmoid,
-            activate_time=10,
-        ),
-        problem=XOR3d(),
-        generation_limit=300,
-        fitness_target=-1e-6
-    )
-
-    # initialize state
-    state = pipeline.setup()
-    # print(state)
-    # run until terminate
-    state, best = pipeline.auto_run(state)
-    # show result
-    pipeline.show(state, best)