fix bugs

2024-07-10 16:50:36 +08:00
parent 4cdac932d3
commit 51cb4695af
8 changed files with 71 additions and 72 deletions
--- a/examples/tmp.py
+++ b/examples/tmp.py
@@ -1,7 +1,7 @@
 import jax, jax.numpy as jnp

 from tensorneat.algorithm import NEAT
-from tensorneat.algorithm.neat import DefaultGenome, RecurrentGenome
+from tensorneat.genome import DefaultGenome, RecurrentGenome

 key = jax.random.key(0)
 genome = DefaultGenome(num_inputs=5, num_outputs=3, max_nodes=100, max_conns=500, init_hidden_layers=(1, 2 ,3))
--- a/network.svg
+++ b/network.svg
@@ -6,7 +6,7 @@
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   <cc:Work>
    <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-07-10T15:27:16.806503</dc:date>
+    <dc:date>2024-07-10T16:50:19.947855</dc:date>
    <dc:format>image/svg+xml</dc:format>
    <dc:creator>
     <cc:Agent>
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 C 423.109949 252.865213 425.312917 251.952714 426.936947 250.328683 
 C 428.560978 248.704652 429.473477 246.501685 429.473477 244.204959 
@@ -381,7 +381,7 @@ C 413.065468 239.705265 412.152969 241.908232 412.152969 244.204959
 C 412.152969 246.501685 413.065468 248.704652 414.689499 250.328683 
 C 416.313529 251.952714 418.516497 252.865213 420.813223 252.865213 
 z
-" clip-path="url(#p80fa8c6777)" style="fill: #0000ff; stroke: #0000ff"/>
+" clip-path="url(#p8fe09283f8)" style="fill: #0000ff; stroke: #0000ff"/>
    <path d="M 420.813223 181.460254 
 C 423.109949 181.460254 425.312917 180.547755 426.936947 178.923724 
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@@ -392,7 +392,7 @@ C 413.065468 168.300306 412.152969 170.503274 412.152969 172.8
 C 412.152969 175.096726 413.065468 177.299694 414.689499 178.923724 
 C 416.313529 180.547755 418.516497 181.460254 420.813223 181.460254 
 z
-" clip-path="url(#p80fa8c6777)" style="fill: #0000ff; stroke: #0000ff"/>
+" clip-path="url(#p8fe09283f8)" style="fill: #0000ff; stroke: #0000ff"/>
    <path d="M 420.813223 110.055295 
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 z
-" clip-path="url(#p80fa8c6777)" style="fill: #0000ff; stroke: #0000ff"/>
+" clip-path="url(#p8fe09283f8)" style="fill: #0000ff; stroke: #0000ff"/>
   </g>
  </g>
 </g>
 <defs>
-  <clipPath id="p80fa8c6777">
+  <clipPath id="p8fe09283f8">
   <rect x="0" y="0" width="460.8" height="345.6"/>
  </clipPath>
 </defs>
--- a/tensorneat/algorithm/neat/init.py
+++ b/tensorneat/algorithm/neat/init.py
@@ -1,4 +1,2 @@
-from .gene import *
-from .genome import *
 from .species import *
 from .neat import NEAT
--- a/tensorneat/algorithm/neat/species/base.py
+++ b/tensorneat/algorithm/neat/species/base.py
@@ -1,5 +1,5 @@
 from tensorneat.common import State, StatefulBaseClass
-from ..genome import BaseGenome
+from tensorneat.genome import BaseGenome


 class BaseSpecies(StatefulBaseClass):
--- a/tensorneat/algorithm/neat/species/default.py
+++ b/tensorneat/algorithm/neat/species/default.py
@@ -1,16 +1,17 @@
 import jax, jax.numpy as jnp
+
+from .base import BaseSpecies
 from tensorneat.common import (
    State,
    rank_elements,
    argmin_with_mask,
    fetch_first,
 )
-from ..genome.utils import (
+from tensorneat.genome.utils import (
    extract_conn_attrs,
    extract_node_attrs,
 )
-from ..genome import BaseGenome
-from .base import BaseSpecies
+from tensorneat.genome import BaseGenome


 """
--- a/tensorneat/genome/base.py
+++ b/tensorneat/genome/base.py
@@ -3,7 +3,7 @@ from typing import Callable, Sequence
 import numpy as np
 import jax
 from jax import vmap, numpy as jnp
-from ..gene import BaseNodeGene, BaseConnGene
+from .gene import BaseNodeGene, BaseConnGene
 from .operations import BaseMutation, BaseCrossover, BaseDistance
 from tensorneat.common import (
    State,
--- a/tensorneat/genome/default.py
+++ b/tensorneat/genome/default.py
@@ -5,8 +5,8 @@ from jax import vmap, numpy as jnp
 import numpy as np
 import sympy as sp

-from . import BaseGenome
-from ..gene import DefaultNodeGene, DefaultConnGene
+from .base import BaseGenome
+from .gene import DefaultNodeGene, DefaultConnGene
 from .operations import DefaultMutation, DefaultCrossover, DefaultDistance
 from .utils import unflatten_conns, extract_node_attrs, extract_conn_attrs

@@ -102,7 +102,7 @@ class DefaultGenome(BaseGenome):
                    state,
                    nodes_attrs[i],
                    ins,
-                    is_output_node=jnp.isin(nodes[0], self.output_idx),  # nodes[0] -> the key of nodes
+                    is_output_node=jnp.isin(nodes[i, 0], self.output_idx),  # nodes[0] -> the key of nodes
                )

                # set new value
--- a/tensorneat/genome/recurrent.py
+++ b/tensorneat/genome/recurrent.py
@@ -3,9 +3,9 @@ from jax import vmap, numpy as jnp
 from .utils import unflatten_conns

 from .base import BaseGenome
+from .gene import DefaultNodeGene, DefaultConnGene
 from .operations import DefaultMutation, DefaultCrossover, DefaultDistance
 from .utils import unflatten_conns, extract_node_attrs, extract_conn_attrs
-from ..gene import DefaultNodeGene, DefaultConnGene

 from tensorneat.common import attach_with_inf