refactoring

src/kartezio/callback.py

@@ -1,24 +1,21 @@
 from abc import ABC
 from datetime import datetime
 from enum import Enum
-from uuid import uuid4
 from typing import Dict
+from uuid import uuid4
 
+import matplotlib.pyplot as plt
 import numpy as np
 
-from kartezio.core.helpers import Observer
 from kartezio.components.genotype import Genotype
 from kartezio.core.decoder import Decoder
-from kartezio.utils.directory import Directory
+from kartezio.core.helpers import Observer
 from kartezio.enums import JSON_ELITE
+from kartezio.utils.directory import Directory
 from kartezio.utils.io import JsonSaver
 from kartezio.utils.json_handler import json_write
 
 
-
-import matplotlib.pyplot as plt
-
-
 def timestamp(ms=True):
     dt = datetime.now()
     if ms:
@@ -34,9 +31,10 @@ def eventid():
     return f"{timestamp()}-{uuid()}".replace(" ", "-")
 
 
-
 class Event:
-    def __init__(self, iteration: int, name: str, content: Dict, force: bool=False):
+    def __init__(
+        self, iteration: int, name: str, content: Dict, force: bool = False
+    ):
         self.iteration = iteration
         self.name = name
         self.content = content
@@ -179,23 +177,27 @@ def on_new_parent(self, iteration, event_content):
 
     def on_evolution_end(self, iteration, event_content):
         self._add_new_line(iteration, event_content)
-        print(f"{self.filename} saved. {len(self.data)} lines, last = {self.data[-1]}")
+        print(
+            f"{self.filename} saved. {len(self.data)} lines, last = {self.data[-1]}"
+        )
         data = np.array(self.data)
         plt.figure()
         plt.plot(data[:, 0], data[:, 1])
         plt.plot(data[:, 0], data[:, 2])
         plt.savefig(f"{self.filename}.png")
-        
+
 
 class CallbackSaveElite(Callback):
     def __init__(self, filename, dataset, preprocessing, fitness):
         super().__init__()
         self.filename = filename
         self.dataset = dataset.__to_dict__()
         self.decoder = None
-        self.preprocessing = preprocessing.__to_dict__() if preprocessing else None
+        self.preprocessing = (
+            preprocessing.__to_dict__() if preprocessing else None
+        )
         self.fitness = fitness.__to_dict__()
-        
+
     def set_decoder(self, decoder: Decoder):
         self.decoder = decoder.__to_dict__()
 
@@ -205,10 +207,12 @@ def on_new_parent(self, iteration, event_content):
             "iteration": iteration,
             "dataset": self.dataset,
             "elite": {
-                "chromosomes": {k: v.tolist() for k, v in elite._chromosomes.items()}
+                "chromosomes": {
+                    k: v.tolist() for k, v in elite._chromosomes.items()
+                }
             },
             "preprocessing": self.preprocessing,
             "decoder": self.decoder,
             "fitness": self.fitness,
         }
-        json_write(self.filename, json_data, indent=None)
+        json_write(self.filename, json_data, indent=None)

src/kartezio/components/base.py

@@ -10,6 +10,7 @@ class Component(ABC):
     Abstract base class for representing a Component in the CGP framework.
     This class provides basic functionalities for components.
     """
+
     def __init__(self):
         """
         Initialize a Component instance.
@@ -48,11 +49,22 @@ class UpdatableComponent(Component, Observer, ABC):
     Inherits from Component and Observer to enable both observation and update capabilities, making it suitable
     for scenarios where a component's internal state must be adjusted during the evolutionary process.
     """
+
     def __init__(self):
         """
         Initialize an UpdatableComponent instance.
         """
         super().__init__()
+        self.n_iterations = None
+        self.stored = None
+
+    def compile(self, n_iterations: int):
+        self.n_iterations = n_iterations
+        self.stored = self._precompute()
+
+    @abstractmethod
+    def _precompute(self):
+        pass
 
 
 class Components:
@@ -114,15 +126,17 @@ def display():
         pprint(Components._registry)
 
 
-
 class Node(Component, ABC):
     """
     Abstract base class for a Node in the CGP framework.
     """
+
     pass
 
 
-def register(component_group: type, component_name: str, replace: bool = False):
+def register(
+    component_group: type, component_name: str, replace: bool = False
+):
     """
     Register a component to the Components registry.
 
@@ -163,4 +177,4 @@ def load_component(component_class: type, json_data: Dict) -> Component:
     Returns:
         Component: An instance of the component created from the given data.
     """
-    return component_class.__from_dict__(json_data)
+    return component_class.__from_dict__(json_data)

src/kartezio/components/dataset.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from kartezio.core.components.base import Component
+from kartezio.components.base import Component
 from kartezio.utils.json_handler import json_read, json_write
 
 

src/kartezio/components/endpoint.py

@@ -38,4 +38,3 @@ def __from_dict__(cls, dict_infos: Dict) -> "Endpoint":
             dict_infos["name"].lower().replace(" ", "_"),
             **dict_infos["args"]
         )
-

src/kartezio/components/genotype.py

@@ -7,10 +7,6 @@
 from kartezio.components.base import Component
 
 
-import copy
-import numpy as np
-from typing import Dict
-
 class Genotype(Component):
     """
     Represents the genotype for Cartesian Genetic Programming (CGP).
@@ -81,8 +77,12 @@ def __from_dict__(cls, dict_infos: Dict) -> "Genotype":
         Returns:
             Genotype: A new Genotype instance created from the given dictionary.
         """
-        assert "chromosomes" in dict_infos, "Expected 'chromosomes' key in dictionary."
-        assert "outputs" in dict_infos["chromosomes"], "Expected 'outputs' key in 'chromosomes' dictionary."
+        assert (
+            "chromosomes" in dict_infos
+        ), "Expected 'chromosomes' key in dictionary."
+        assert (
+            "outputs" in dict_infos["chromosomes"]
+        ), "Expected 'outputs' key in 'chromosomes' dictionary."
         n_outputs = len(dict_infos["chromosomes"]["outputs"])
         genotype = cls(n_outputs)
         for key, value in dict_infos["chromosomes"].items():
@@ -97,4 +97,3 @@ def clone(self) -> "Genotype":
             Genotype: A cloned instance of the genotype.
         """
         return copy.deepcopy(self)
-

src/kartezio/components/initializer.py

@@ -2,16 +2,16 @@
 from typing import Dict
 
 from kartezio.components.base import register
-from kartezio.core.decoder import Adapter
 from kartezio.components.genotype import Genotype
+from kartezio.core.decoder import Adapter
 from kartezio.mutation.base import Mutation
 
-
+"""
 @register(Mutation, "all_random")
 class RandomInit(Mutation):
-    """
+    '''
     Can be used to initialize genome (genome) randomly
-    """
+    '''
 
     @classmethod
     def __from_dict__(cls, dict_infos: Dict) -> "Mutation":
@@ -32,9 +32,11 @@ def mutate(self, genotype):
         return genotype
 
     def random(self):
-        genotype = self.adapter.new()
+        genotype = self.adapter.new_genotype()
         return self.mutate(genotype)
 
+"""
+
 
 @register(Mutation, "copy")
 class CopyGenotype(Mutation):
@@ -51,7 +53,7 @@ def mutate(self, genotype):
 
 
 @register(Mutation, "all_random_poly")
-class MutationAllRandomPoly(Mutation):
+class RandomInit(Mutation):
     """
     Can be used to initialize genome (genome) randomly
     """

src/kartezio/components/library.py

@@ -5,11 +5,10 @@
 import numpy as np
 from tabulate import tabulate
 
-from kartezio.components.base import Node, Components, Component, register
+from kartezio.components.base import Component, Components, Node, register
 from kartezio.core.types import KType
 
 
-
 class Primitive(Node, ABC):
     """
     Primitive function called inside the CGP Graph.
@@ -22,12 +21,10 @@ def __init__(self, inputs: List[KType], output: KType, n_parameters: int):
         self.arity = len(inputs)
         self.n_parameters = n_parameters
 
-
-
     @classmethod
     def __from_dict__(cls, dict_infos: Dict) -> "Primitive":
         return Components.instantiate("Primitive", dict_infos["name"])
-    
+
 
 class Library(Component, ABC):
     def __init__(self, rtype):