initial commit in branch developing

.idea/.gitignore

@@ -0,0 +1,8 @@
+# 默认忽略的文件
+/shelf/
+/workspace.xml
+# 基于编辑器的 HTTP 客户端请求
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml

.idea/deployment.xml

@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="PublishConfigData" remoteFilesAllowedToDisappearOnAutoupload="false">
+    <serverData>
+      <paths name="dengsh@10.16.33.46:22">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+      <paths name="lishuang@10.16.2.22:22">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+      <paths name="lishuang@10.16.2.22:22 password">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+      <paths name="root@124.71.72.72:22">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+      <paths name="root@124.71.72.72:22 password">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+    </serverData>
+  </component>
+</project>

.idea/inspectionProfiles/Project_Default.xml

@@ -0,0 +1,34 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="DuplicatedCode" enabled="false" level="WEAK WARNING" enabled_by_default="false">
+      <Languages>
+        <language minSize="97" name="Python" />
+      </Languages>
+    </inspection_tool>
+    <inspection_tool class="PyPep8Inspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="E722" />
+        </list>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPep8NamingInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="N812" />
+          <option value="N801" />
+          <option value="N806" />
+          <option value="N803" />
+        </list>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredIdentifiers">
+        <list>
+          <option value="tests.jax_learn_2022_10_23.*" />
+        </list>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>

.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="jax_env" project-jdk-type="Python SDK" />
+</project>

.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/neatax.iml" filepath="$PROJECT_DIR$/.idea/neatax.iml" />
+    </modules>
+  </component>
+</project>

.idea/neatax.iml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="jax_env" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</module>

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

algorithms/neat/genome/genome.py

@@ -193,6 +193,13 @@ def pop_analysis(pop_nodes, pop_connections, input_keys, output_keys):
     return res
 
 
+@jit
+def count(nodes, connections):
+    node_cnt = jnp.sum(~jnp.isnan(nodes[:, 0]))
+    connections_cnt = jnp.sum(~jnp.isnan(connections[0, :, :]))
+    return node_cnt, connections_cnt
+
+
 @jit
 def add_node(new_node_key: int, nodes: Array, connections: Array,
              bias: float = 0.0, response: float = 1.0, act: int = 0, agg: int = 0) -> Tuple[Array, Array]:

algorithms/neat/pipeline.py

@@ -7,7 +7,7 @@ import numpy as np
 from .species import SpeciesController
 from .genome import expand, expand_single
 from .function_factory import FunctionFactory
-
+from .genome.genome import count
 
 class Pipeline:
     """

examples/jax_playground.py

@@ -1,21 +1,5 @@
-import jax
 import jax.numpy as jnp
-import numpy as np
-from jax import random
-from jax import vmap, jit
-from functools import partial
 
-from examples.time_utils import using_cprofile
+EMPTY_NODE = jnp.full((1, 5), jnp.nan)
 
-
+print(EMPTY_NODE)
-@jit
-def func(x, y):
-    return x + y
-
-
-a, b, c = jnp.array([1]), jnp.array([2]), jnp.array([3])
-li = [a, b, c]
-
-cpu_li = jax.device_get(li)
-
-print(cpu_li)

examples/xor.py

@@ -6,35 +6,14 @@ from time_utils import using_cprofile
 from problems import Sin, Xor, DIY
 
 
-# xor_inputs = np.array([[0, 0], [0, 1], [1, 0], [1, 1]], dtype=np.float32)
-# xor_outputs = np.array([[0], [1], [1], [0]])
-#
-#
-# def evaluate(forward_func: Callable) -> List[float]:
-#     """
-#     :param forward_func: (4: batch, 2: input size) -> (pop_size, 4: batch, 1: output size)
-#     :return:
-#     """
-#     outs = forward_func(xor_inputs)
-#     outs = jax.device_get(outs)
-#     fitnesses = 4 - np.sum((outs - xor_outputs) ** 2, axis=(1, 2))
-#     return fitnesses.tolist()  # returns a list
-
-
 # @using_cprofile
 @partial(using_cprofile, root_abs_path='/mnt/e/neat-jax/', replace_pattern="/mnt/e/neat-jax/")
 def main():
     config = Configer.load_config()
-    # config.neat.population.pop_size = 50
     problem = Xor()
-    # problem = Sin()
-    # problem = DIY(func=lambda x: (np.sin(x) + np.exp(x) - x ** 2) / (np.cos(x) + np.sqrt(x)) - np.log(x + 1))
     problem.refactor_config(config)
     pipeline = Pipeline(config, seed=0)
-    best_nodes, best_connections = pipeline.auto_run(problem.evaluate)
+    pipeline.auto_run(problem.evaluate)
-    # print(best_nodes, best_connections)
-    # func = pipeline.function_factory.ask_batch_forward(best_nodes, best_connections)
-    # problem.print(func)
 
 
 if __name__ == '__main__':

utils/default_config.json

@@ -57,9 +57,9 @@
             "compatibility_weight_coefficient": 0.5,
             "single_structural_mutation": "False",
             "conn_add_prob": 0.5,
-            "conn_delete_prob": 0.5,
+            "conn_delete_prob": 0,
             "node_add_prob": 0.2,
-            "node_delete_prob": 0.2
+            "node_delete_prob": 0
         },
         "species": {
             "compatibility_threshold": 2.5,