fix bugs in hyperneat;

related to https://github.com/EMI-Group/tensorneat/issues/17

src/tensorneat/algorithm/hyperneat/substrate/default.py

@@ -1,4 +1,4 @@
-from jax import vmap
+from jax import vmap, numpy as jnp
 import numpy as np
 
 from .base import BaseSubstrate
@@ -12,9 +12,9 @@ class DefaultSubstrate(BaseSubstrate):
     def __init__(self, num_inputs, num_outputs, coors, nodes, conns):
         self.inputs = num_inputs
         self.outputs = num_outputs
-        self.coors = np.array(coors)
-        self.nodes = np.array(nodes)
-        self.conns = np.array(conns)
+        self.coors = jnp.array(coors)
+        self.nodes = jnp.array(nodes)
+        self.conns = jnp.array(conns)
 
     def make_nodes(self, query_res):
         return self.nodes
@@ -22,7 +22,8 @@ class DefaultSubstrate(BaseSubstrate):
     def make_conns(self, query_res):
         # change weight of conns
         # the last column is the weight
-        return self.conns.at[:, -1].set(query_res)
+        # print(f"{self.conns.shape=}, {query_res.shape=}")
+        return self.conns.at[:, -1].set(query_res.flatten())
 
     @property
     def query_coors(self):

src/tensorneat/algorithm/hyperneat/substrate/full.py

@@ -63,7 +63,7 @@ def analysis_substrate(input_coors, output_coors, hidden_coors):
     )  # input_idx, output_idx, weight
     conns[:, :2] = correspond_keys
 
-    print(query_coors, nodes, conns)
+    # print(query_coors, nodes, conns)
     return query_coors, nodes, conns