This commit is related to issue: https://github.com/EMI-Group/tensorneat/issues/11

1. Add origin_node and origin_conn.
2. Change the behavior of crossover and mutation. Now, TensorNEAT will use all fix_attrs(include historical marker if it has one) as identifier for gene in crossover and distance calculation.
3. Other slightly change.
4. Add two related examples: xor_origin and hopper_origin
5. Add related test file.

src/tensorneat/genome/utils.py

@@ -2,6 +2,7 @@ import jax
 from jax import vmap, numpy as jnp
 import numpy as np
 
+from .gene import BaseGene
 from tensorneat.common import fetch_first, I_INF
 
 
@@ -38,49 +39,27 @@ def valid_cnt(nodes_or_conns):
     return jnp.sum(~jnp.isnan(nodes_or_conns[:, 0]))
 
 
-def extract_node_attrs(node):
+def extract_gene_attrs(gene: BaseGene, gene_array):
     """
-    node: Array(NL, )
-    extract the attributes of a node
+    extract the custom attributes of the gene
     """
-    return node[1:]  # 0 is for idx
+    return gene_array[len(gene.fixed_attrs) :]
 
 
-def set_node_attrs(node, attrs):
+def set_gene_attrs(gene: BaseGene, gene_array, attrs):
     """
-    node: Array(NL, )
-    attrs: Array(NL-1, )
-    set the attributes of a node
+    set the custom attributes of the gene
     """
-    return node.at[1:].set(attrs)  # 0 is for idx
+    return gene_array.at[len(gene.fixed_attrs) :].set(attrs)
 
 
-def extract_conn_attrs(conn):
-    """
-    conn: Array(CL, )
-    extract the attributes of a connection
-    """
-    return conn[2:]  # 0, 1 is for in-idx and out-idx
-
-
-def set_conn_attrs(conn, attrs):
-    """
-    conn: Array(CL, )
-    attrs: Array(CL-2, )
-    set the attributes of a connection
-    """
-    return conn.at[2:].set(attrs)  # 0, 1 is for in-idx and out-idx
-
-
-def add_node(nodes, new_key: int, attrs):
+def add_node(nodes, fix_attrs, custom_attrs):
     """
     Add a new node to the genome.
     The new node will place at the first NaN row.
     """
-    exist_keys = nodes[:, 0]
-    pos = fetch_first(jnp.isnan(exist_keys))
-    new_nodes = nodes.at[pos, 0].set(new_key)
-    return new_nodes.at[pos, 1:].set(attrs)
+    pos = fetch_first(jnp.isnan(nodes[:, 0]))
+    return nodes.at[pos].set(jnp.concatenate((fix_attrs, custom_attrs)))
 
 
 def delete_node_by_pos(nodes, pos):
@@ -91,15 +70,13 @@ def delete_node_by_pos(nodes, pos):
     return nodes.at[pos].set(jnp.nan)
 
 
-def add_conn(conns, i_key, o_key, attrs):
+def add_conn(conns, fix_attrs, custom_attrs):
     """
     Add a new connection to the genome.
     The new connection will place at the first NaN row.
     """
-    con_keys = conns[:, 0]
-    pos = fetch_first(jnp.isnan(con_keys))
-    new_conns = conns.at[pos, 0:2].set(jnp.array([i_key, o_key]))
-    return new_conns.at[pos, 2:].set(attrs)
+    pos = fetch_first(jnp.isnan(conns[:, 0]))
+    return conns.at[pos].set(jnp.concatenate((fix_attrs, custom_attrs)))
 
 
 def delete_conn_by_pos(conns, pos):