evonet 0.1.0.dev8__tar.gz → 0.1.0.dev10__tar.gz

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: evonet
-Version: 0.1.0.dev8
+Version: 0.1.0.dev10
 Summary: Evolvable neural network core for integration with EvoLib
 Author-email: EvoLib <evolib@dismail.de>
 License: MIT License
@@ -39,6 +39,7 @@ Requires-Dist: pyyaml>=6.0
 Requires-Dist: pandas>=2.3.0
 Requires-Dist: pydantic<3.0,>=2.7
 Requires-Dist: graphviz>=0.20.1
+Requires-Dist: matplotlib
 Provides-Extra: dev
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: types-PyYAML; extra == "dev"

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/evonet/activation.py

@@ -203,4 +203,5 @@ ACTIVATIONS: dict[str, Callable] = {
     "softplus": softplus,
     "softsign": softsign,
     "hard_sigmoid": hard_sigmoid,
+    "softmax": softmax,
 }

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/evonet/core.py

@@ -9,11 +9,13 @@ export interfaces.
 
 from __future__ import annotations
 
+from pathlib import Path
 from typing import Literal, Optional
 
 import graphviz
 import numpy as np
 
+from evonet.activation import softmax as softmax_vec
 from evonet.connection import Connection
 from evonet.enums import ConnectionType, NeuronRole, RecurrentKind
 from evonet.layer import Layer
@@ -274,10 +276,28 @@ class Nnet:
 
         # Feed-forward by layers: activate first, then propagate non-recurrent edges
         for layer in self.layers:
+
+            # Apply softmax to all neurons with activation_name == "softmax"
+            softmax_neurons = [
+                n for n in layer.neurons if n.activation_name == "softmax"
+            ]
+            if softmax_neurons:
+                if len(softmax_neurons) >= 2:
+                    # Normal softmax behaviour
+                    totals = [n.input + n.bias for n in softmax_neurons]
+                    probabilities = softmax_vec(totals)
+                    for n, p in zip(softmax_neurons, probabilities):
+                        n.output = float(p)
+                else:
+                    # Fallback: single softmax neuron acts like identity
+                    n = softmax_neurons[0]
+                    n.output = n.input + n.bias
+
             # Activate all neurons in this layer
             for n in layer.neurons:
-                total = n.input + n.bias
-                n.output = n.activation(total)
+                if n.activation_name != "softmax":
+                    total = n.input + n.bias
+                    n.output = n.activation(total)
 
             # Propagate to targets (exclude recurrent edges)
             for n in layer.neurons:
@@ -310,7 +330,7 @@ class Nnet:
             f"{total_connections} connections "
         )
 
-    def print_graph(
+    def plot(
         self,
         name: str,
         engine: str = "dot",
@@ -344,7 +364,7 @@ class Nnet:
             ratio="fill",
             splines="spline",
             size="6.68,5!",
-            dpi="200",
+            dpi="600",
         )
         dot.node_attr.update(
             shape="circle", style="filled", fixedsize="shape", width="1.8"
@@ -530,3 +550,55 @@ class Nnet:
 
         for b, n in zip(flat, targets):
             n.bias = float(b)
+
+    def save(self, path: str) -> None:
+        """
+        Save this network to a file.
+
+        The file format is chosen automatically based on the extension:
+        - .yaml / .yml --> YAML (human-readable, recommended)
+        - .json        --> JSON (machine-friendly)
+
+        Args:
+            path (str): Output file path.
+        """
+
+        from . import serialization  # local import to avoid circular import
+
+        suffix = Path(path).suffix.lower()
+        if suffix in (".yaml", ".yml"):
+            serialization.save_yaml(self, path)
+        elif suffix == ".json":
+            serialization.save_json(self, path)
+        else:
+            raise ValueError(
+                f"Unsupported file extension '{suffix}'. Use .yaml, .yml or .json"
+            )
+
+    @classmethod
+    def load(cls, path: str) -> "Nnet":
+        """
+        Load a network from a file.
+
+        The file format is chosen automatically based on the extension:
+        - .yaml / .yml --> YAML
+        - .json        --> JSON
+
+        Args:
+            path (str): Path to the serialized network file.
+
+        Returns:
+            Nnet: The reconstructed network.
+        """
+
+        from . import serialization  # local import to avoid circular import
+
+        suffix = Path(path).suffix.lower()
+        if suffix in (".yaml", ".yml"):
+            return serialization.load_yaml(path)
+        elif suffix == ".json":
+            return serialization.load_json(path)
+        else:
+            raise ValueError(
+                f"Unsupported file extension '{suffix}'. Use .yaml, .yml or .json"
+            )

evonet-0.1.0.dev10/evonet/core_mit_plot_simple.py

@@ -0,0 +1,645 @@
+# SPDX-License-Identifier: MIT
+"""
+Core class for evolvable neural networks.
+
+Manages neurons, layers, and connections with explicit topology. Supports forward passes
+with optional recurrent connections across time steps, mutation/crossover hooks, and
+export interfaces.
+"""
+
+from __future__ import annotations
+
+from typing import Literal, Optional
+
+import graphviz
+import numpy as np
+import matplotlib.pyplot as plt
+
+from evonet.activation import softmax as softmax_vec
+from evonet.connection import Connection
+from evonet.enums import ConnectionType, NeuronRole, RecurrentKind
+from evonet.layer import Layer
+from evonet.neuron import Neuron
+
+
+class Nnet:
+    """
+    Evolvable neural network with explicit layered topology.
+
+    Attributes:
+        layers (list[Layer]): Ordered list of network layers.
+    """
+
+    def __init__(self) -> None:
+        self.layers: list[Layer] = []
+
+    @property
+    def num_weights(self) -> int:
+        """Number of connections in the network (no allocation)."""
+        return len(self.get_all_connections())
+
+    @property
+    def num_biases(self) -> int:
+        """
+        Return the number of trainable biases (excludes input neurons).
+
+        Inputs are feature holders and have no trainable bias in this design.
+        """
+        count = 0
+        for layer in self.layers:
+            for neuron in layer.neurons:
+                if neuron.role is not NeuronRole.INPUT:
+                    count += 1
+        return count
+
+    @property
+    def num_params(self) -> int:
+        """Total parameter count = weights + biases."""
+        return self.num_weights + self.num_biases
+
+    def add_layer(self, count: int = 1) -> int:
+        """
+        Append one or more empty layers to the network.
+
+        Args:
+            count (int): Number of layers to add (must be > 0).
+
+        Returns:
+            int: Index of the last added layer.
+
+        Raises:
+            ValueError: If count is not positive.
+        """
+
+        if count <= 0:
+            raise ValueError("Number of layers must be greater then zero")
+
+        for _ in range(count):
+            self.layers.append(Layer())
+
+        return len(self.layers) - 1
+
+    def insert_layer(self, index: int) -> None:
+        """
+        Insert an empty layer at a given index.
+
+        Args:
+            index (int): Position to insert the new layer (0 = before input).
+
+        Raises:
+            ValueError: If index is out of bounds.
+        """
+
+        if not (0 <= index <= len(self.layers)):
+            raise ValueError(f"insert_layer: index {index} out of bounds.")
+        self.layers.insert(index, Layer())
+
+    def add_neuron(
+        self,
+        layer_idx: int | None = None,
+        activation: str = "tanh",
+        bias: float = 0.0,
+        label: str = "",
+        role: NeuronRole = NeuronRole.HIDDEN,
+        count: int = 1,
+        connection_init: Literal["random", "zero", "none"] = "random",
+        recurrent: Optional[set[RecurrentKind]] = None,
+    ) -> list[Neuron]:
+        """
+        Add one or more neurons to the network.
+
+        Args:
+            layer_idx: Target layer index. Defaults to last layer.
+            activation: Activation function name.
+            bias: Initial bias value.
+            label: Optional label.
+            role: Role of the neuron (INPUT, HIDDEN, OUTPUT).
+            count: Number of neurons to add (default: 1).
+            connection_init:
+                "random" – connect with random weights (feedforward + recurrent)
+                "zero"   – connect with weight 0.0 (feedforward + recurrent)
+                "none"   – do not create connections (feedforward + recurrent)
+            recurrent: Optional recurrent connection types.
+
+        Returns:
+            list[Neuron]: List of added neurons.
+        """
+        if layer_idx is None:
+            layer_idx = len(self.layers) - 1  # Add neuron to last layer
+
+        if layer_idx < 0:
+            raise ValueError(f"Layer index must be >= 0 (got {layer_idx})")
+        if layer_idx >= len(self.layers):
+            raise ValueError(f"Layer index out of bounds: {layer_idx}")
+
+        target_layer = self.layers[layer_idx]
+        new_neurons: list[Neuron] = []
+
+        # Create neurons without connections
+        for _ in range(count):
+            neuron = Neuron(activation=activation, bias=bias)
+            neuron.role = role
+            neuron.label = label
+            target_layer.neurons.append(neuron)
+            new_neurons.append(neuron)
+
+        # Weights based on init mode
+        weight_map = {"random": None, "zero": 0.0, "none": None}
+        if connection_init not in weight_map:
+            raise ValueError(f"Invalid connection_init: {connection_init}")
+        weight = weight_map[connection_init]
+
+        skip_connections = connection_init == "none"
+
+        # Connect to previous layer
+        if not skip_connections and layer_idx > 0:
+            for prev_neuron in self.layers[layer_idx - 1].neurons:
+                for n in new_neurons:
+                    self.add_connection(prev_neuron, n, weight=weight)
+
+        # Connect to next layer (hidden only)
+        if (
+            not skip_connections
+            and role == NeuronRole.HIDDEN
+            and layer_idx < len(self.layers) - 1
+        ):
+            for next_neuron in self.layers[layer_idx + 1].neurons:
+                for n in new_neurons:
+                    self.add_connection(n, next_neuron, weight=weight)
+
+        # Recurrent connections
+        if recurrent and not skip_connections:
+            if RecurrentKind.DIRECT in recurrent:
+                for n in new_neurons:
+                    if n.role == NeuronRole.HIDDEN:
+                        self.add_connection(
+                            n, n, weight=weight, conn_type=ConnectionType.RECURRENT
+                        )
+
+            if RecurrentKind.LATERAL in recurrent:
+                full_layer = list(self.layers[layer_idx].neurons)
+                for src in full_layer:
+                    for dst in new_neurons:
+                        if src is not dst:
+                            self.add_connection(
+                                src,
+                                dst,
+                                weight=weight,
+                                conn_type=ConnectionType.RECURRENT,
+                            )
+
+            if RecurrentKind.INDIRECT in recurrent:
+                for src in new_neurons:
+                    for lower_layer in self.layers[1:layer_idx]:
+                        for dst in lower_layer.neurons:
+                            self.add_connection(
+                                src,
+                                dst,
+                                weight=weight,
+                                conn_type=ConnectionType.RECURRENT,
+                            )
+                for higher_layer in self.layers[layer_idx + 1 :]:
+                    for src in higher_layer.neurons:
+                        for dst in new_neurons:
+                            self.add_connection(
+                                src,
+                                dst,
+                                weight=weight,
+                                conn_type=ConnectionType.RECURRENT,
+                            )
+
+        return new_neurons
+
+    def add_connection(
+        self,
+        source: Neuron,
+        target: Neuron,
+        weight: float | None = None,
+        conn_type: ConnectionType = ConnectionType.STANDARD,
+    ) -> None:
+        """
+        Create a directed connection between two neurons.
+
+        Args:
+            source (Neuron): Source neuron.
+            target (Neuron): Target neuron.
+            weight (float | None): Initial weight. If None, random value is used.
+            conn_type (ConnectionType): Type of connection (e.g. standard, recurrent).
+        """
+
+        if weight is None:
+            weight = np.random.randn() * 0.5
+
+        conn = Connection(source, target, weight=weight, conn_type=conn_type)
+        source.outgoing.append(conn)
+        target.incoming.append(conn)
+
+    def reset(self, full: bool = False) -> None:
+        """Reset all neurons (clears input, output, and caches)."""
+        for layer in self.layers:
+            for neuron in layer.neurons:
+                neuron.reset(full=full)
+
+    def calc(self, input_values: list[float]) -> list[float]:
+        """
+        Perform a forward pass through the network.
+
+        Args:
+            input_values (list[float]): Input vector (must match input layer size).
+
+        Returns:
+            list[float]: Output values from the last layer.
+
+        Raises:
+            AssertionError: If input size does not match input layer.
+        """
+
+        # Save LAST OUTPUT
+        for layer in self.layers:
+            for neuron in layer.neurons:
+                neuron.last_output = neuron.output
+
+        self.reset()
+
+        # Set inputs
+        input_layer = self.layers[0]
+        assert len(input_layer.neurons) == len(input_values)
+        for i, n in enumerate(input_layer.neurons):
+            n.input = float(input_values[i])
+
+        # Preload recurrent contributions from previous time step (last_output)
+        for layer in self.layers:
+            for n in layer.neurons:
+                for c in n.incoming:
+                    if c.type is ConnectionType.RECURRENT:
+                        c.target.input += c.weight * c.source.last_output
+
+        # Feed-forward by layers: activate first, then propagate non-recurrent edges
+        for layer in self.layers:
+
+            # Apply softmax to all neurons with activation_name == "softmax"
+            softmax_neurons = [
+                n for n in layer.neurons if n.activation_name == "softmax"
+            ]
+            if softmax_neurons:
+                if len(softmax_neurons) >= 2:
+                    # Normal softmax behaviour
+                    totals = [n.input + n.bias for n in softmax_neurons]
+                    probabilities = softmax_vec(totals)
+                    for n, p in zip(softmax_neurons, probabilities):
+                        n.output = float(p)
+                else:
+                    # Fallback: single softmax neuron acts like identity
+                    n = softmax_neurons[0]
+                    n.output = n.input + n.bias
+
+            # Activate all neurons in this layer
+            for n in layer.neurons:
+                if n.activation_name != "softmax":
+                    total = n.input + n.bias
+                    n.output = n.activation(total)
+
+            # Propagate to targets (exclude recurrent edges)
+            for n in layer.neurons:
+                for c in n.outgoing:
+                    if c.type is not ConnectionType.RECURRENT:
+                        c.target.input += c.weight * n.output
+
+        return [n.output for n in self.layers[-1].neurons]
+
+    def get_all_neurons(self) -> list[Neuron]:
+        """Return all neurons in all layers (flattened)."""
+        return [n for layer in self.layers for n in layer.neurons]
+
+    def get_all_connections(self) -> list[Connection]:
+        """Return all outgoing connections in the network."""
+        return [c for n in self.get_all_neurons() for c in n.outgoing]
+
+    def __repr__(self) -> str:
+        total_neurons = sum(len(layer.neurons) for layer in self.layers)
+        input_neurons = len(self.layers[0].neurons) if self.layers else 0
+        output_neurons = len(self.layers[-1].neurons) if len(self.layers) > 1 else 0
+        hidden_neurons = total_neurons - input_neurons - output_neurons
+
+        total_connections = len(self.get_all_connections())
+
+        return (
+            f"<Nnet | {len(self.layers)} layers, "
+            f"{total_neurons} neurons (I:{input_neurons} H:{hidden_neurons} "
+            f"O:{output_neurons}), "
+            f"{total_connections} connections "
+        )
+
+    def print_graph(
+        self,
+        name: str,
+        engine: str = "dot",
+        labels_on: bool = True,
+        colors_on: bool = True,
+        thickness_on: bool = False,
+        fillcolors_on: bool = False,
+    ) -> None:
+        """
+        Render a visual representation of the network using Graphviz.
+
+        Args:
+            name (str): Output file name (without extension).
+            engine (str): Graphviz layout engine (e.g., 'dot', 'neato').
+            labels_on (bool): Whether to show edge weights as labels.
+            colors_on (bool): Whether to color edges by sign.
+            thickness_on (bool): Whether to scale edge thickness by weight.
+            fillcolors_on (bool): Whether to color neurons by role.
+        """
+
+        if not self.layers:
+            print("No layers to visualize.")
+            return
+
+        dot = graphviz.Digraph(name=name, format="png", engine=engine)
+        dot.graph_attr.update(
+            bgcolor="white",
+            rankdir="LR",
+            overlap="prism",
+            sep="15",
+            ratio="fill",
+            splines="spline",
+            size="6.68,5!",
+            dpi="600",
+        )
+        dot.node_attr.update(
+            shape="circle", style="filled", fixedsize="shape", width="1.8"
+        )
+        dot.edge_attr.update(arrowsize="0.8")
+
+        # Add neurons with coordinates (x = layer, y = index)
+        for layer_idx, layer in enumerate(self.layers):
+            for neuron_idx, neuron in enumerate(layer.neurons):
+                if neuron.role.name == "INPUT":
+                    fillcolor = "lightblue" if fillcolors_on else "white"
+                elif neuron.role.name == "OUTPUT":
+                    fillcolor = "orange" if fillcolors_on else "white"
+                else:
+                    fillcolor = "lightgreen" if fillcolors_on else "white"
+
+                label = (
+                    f"{neuron.label or neuron.role.name}({layer_idx})\n"
+                    f"In: {neuron.input:.3f}\n"
+                    f"Out: {neuron.output:.3f}\n"
+                    f"LastOut: {neuron.last_output:.3f}\n"
+                    f"Bias: {neuron.bias:.3f}\n"
+                    f"{neuron.activation_name}"
+                )
+
+                pos = f"{layer_idx},{-neuron_idx}!"
+                dot.node(
+                    name=neuron.id,
+                    label=label,
+                    fillcolor=fillcolor,
+                    pos=pos,
+                )
+
+        # Add edges
+        for conn in self.get_all_connections():
+            label = f"{conn.weight:.2f}" if labels_on else ""
+            color = (
+                "green"
+                if colors_on and conn.weight >= 0
+                else "red" if colors_on else "black"
+            )
+            penwidth = (
+                str(max(1, min(5, abs(conn.weight * 5)))) if thickness_on else "1"
+            )
+            style = "dashed" if conn.type.name == "RECURRENT" else "solid"
+
+            dot.edge(
+                conn.source.id,
+                conn.target.id,
+                label=label,
+                color=color,
+                penwidth=penwidth,
+                style=style,
+            )
+
+        dot.render(name, cleanup=True)
+
+    def plot_simple(
+        net,
+        show_weights: bool = False,
+        show_values: bool = True,
+        path: str | None = None,
+    ) -> None:
+        """
+        Visualize the network in a simple layered layout using Matplotlib.
+
+        Args:
+            net: The Nnet object to visualize.
+            show_weights (bool): If True, draw weight values on edges.
+            show_values (bool): If True, neuron output values are shown,
+                                else neuron indices.
+            path (str | None): If given, save the plot to this path instead
+                               of displaying.
+        """
+
+        fig, ax = plt.subplots(figsize=(8, 6))
+        ax.set_aspect("equal")
+        ax.axis("off")
+
+        neuron_positions: dict = {}
+
+        # Place neurons
+        for layer_idx, layer in enumerate(net.layers):
+            y_positions = list(range(len(layer.neurons)))
+            offset = (
+                max(len(layer.neurons) for layer in net.layers) - len(y_positions)
+            ) / 2.0
+
+            for neuron_idx, neuron in enumerate(layer.neurons):
+                x, y = layer_idx, neuron_idx + offset
+                neuron_positions[neuron] = (x, y)
+
+                ax.scatter(
+                    x,
+                    y,
+                    c="royalblue",
+                    s=400,
+                    zorder=3,
+                    edgecolors="white",
+                    linewidths=1.5,
+                )
+
+                label = f"{neuron.output:.2f}" if show_values else str(neuron_idx)
+                ax.text(
+                    x,
+                    y,
+                    label,
+                    ha="center",
+                    va="center",
+                    color="white",
+                    fontsize=9,
+                    zorder=4,
+                )
+
+        # Draw connections
+        for layer in net.layers[1:]:
+            for neuron in layer.neurons:
+                x2, y2 = neuron_positions[neuron]
+                for conn in neuron.incoming:
+                    x1, y1 = neuron_positions[conn.source]
+                    style = "--" if getattr(conn, "recurrent", False) else "-"
+                    color = "crimson" if getattr(conn, "recurrent", False) else "gray"
+                    ax.plot(
+                        [x1, x2],
+                        [y1, y2],
+                        color=color,
+                        linestyle=style,
+                        alpha=0.7,
+                        zorder=1,
+                    )
+
+                    if show_weights:
+                        xm, ym = (x1 + x2) / 2, (y1 + y2) / 2
+                        ax.text(
+                            xm,
+                            ym,
+                            f"{conn.weight:.2f}",
+                            fontsize=7,
+                            color="black",
+                            alpha=0.6,
+                        )
+
+        plt.tight_layout()
+
+        if path:
+            plt.savefig(path, dpi=150)
+            plt.close(fig)
+        else:
+            plt.show()
+
+    def _build_index_map(self) -> dict[Neuron, tuple[int, int]]:
+        """Build a mapping from neuron -> (layer_idx, neuron_idx) for O(1) lookups."""
+        index_map: dict[Neuron, tuple[int, int]] = {}
+        for layer_idx, layer in enumerate(self.layers):
+            for neuron_idx, neuron in enumerate(layer.neurons):
+                index_map[neuron] = (layer_idx, neuron_idx)
+        return index_map
+
+    def get_weights(self) -> np.ndarray:
+        """
+        Return all connection weights as a flat vector in a deterministic order.
+
+        Returns:
+            np.ndarray: 1D array of connection weights.
+
+        Order key:
+            (src_layer_idx, src_neuron_idx, dst_layer_idx,
+            dst_neuron_idx, connection_type)
+        """
+        conns = self.get_all_connections()
+        if not conns:
+            return np.empty(0, dtype=float)
+
+        index_map = self._build_index_map()
+
+        def sort_key(c: Connection) -> tuple[int, int, int, int, int]:
+            src_layer_idx, src_neuron_idx = index_map[c.source]
+            dst_layer_idx, dst_neuron_idx = index_map[c.target]
+            return (
+                src_layer_idx,
+                src_neuron_idx,
+                dst_layer_idx,
+                dst_neuron_idx,
+                int(c.type.value),
+            )
+
+        conns_sorted = sorted(conns, key=sort_key)
+        return np.array([c.weight for c in conns_sorted], dtype=float)
+
+    def set_weights(self, flat: np.ndarray) -> None:
+        """
+        Set all connection weights from a flat vector using the same deterministic order
+        as `get_weights()`.
+
+        Args:
+            flat (np.ndarray): Flat array of weights (must match number of connections).
+
+        Raises:
+            ValueError: If the length of the array does not match.
+        """
+        flat = np.asarray(flat, dtype=float).ravel()
+
+        conns = self.get_all_connections()
+        if not conns and flat.size == 0:
+            return
+
+        index_map = self._build_index_map()
+
+        def sort_key(c: Connection) -> tuple[int, int, int, int, int]:
+            src_layer_idx, src_neuron_idx = index_map[c.source]
+            dst_layer_idx, dst_neuron_idx = index_map[c.target]
+            return (
+                src_layer_idx,
+                src_neuron_idx,
+                dst_layer_idx,
+                dst_neuron_idx,
+                int(c.type.value),
+            )
+
+        conns_sorted = sorted(conns, key=sort_key)
+
+        if flat.size != len(conns_sorted):
+            raise ValueError(
+                f"Length mismatch for weights: expected {len(conns_sorted)}, "
+                f"got {flat.size}."
+            )
+
+        for weight_value, conn in zip(flat, conns_sorted):
+            conn.weight = float(weight_value)
+
+    def get_biases(self) -> np.ndarray:
+        """
+        Return all trainable biases as a flat vector (excluding input neurons).
+
+        Returns:
+            np.ndarray: Bias vector.
+
+        Order:
+            (layer_index, neuron_index) over all non-input neurons.
+        """
+
+        if not self.layers:
+            return np.empty(0, dtype=float)
+
+        biases: list[float] = []
+        for _, layer in enumerate(self.layers):
+            for _, neuron in enumerate(layer.neurons):
+                if neuron.role is not NeuronRole.INPUT:
+                    biases.append(neuron.bias)
+        return np.asarray(biases, dtype=float)
+
+    def set_biases(self, flat: np.ndarray) -> None:
+        """
+        Set all neuron biases (excluding input neurons) from a flat vector using the
+        same ordering as `get_biases()`.
+
+        Args:
+            flat (np.ndarray): Bias values in deterministic order.
+
+        Raises:
+            ValueError: If length does not match the number of biases.
+        """
+        flat = np.asarray(flat, dtype=float).ravel()
+
+        # Collect non-input neurons in deterministic order
+        targets: list[Neuron] = []
+        for _, layer in enumerate(self.layers):
+            for _, neuron in enumerate(layer.neurons):
+                if neuron.role is not NeuronRole.INPUT:
+                    targets.append(neuron)
+
+        if flat.size != len(targets):
+            raise ValueError(
+                f"Length mismatch for biases: expected {len(targets)}, got {flat.size}."
+            )
+
+        for b, n in zip(flat, targets):
+            n.bias = float(b)

evonet-0.1.0.dev10/evonet/serialization.py

@@ -0,0 +1,171 @@
+# SPDX-License-Identifier: MIT
+"""
+Serialization utilities for EvoNet networks.
+
+This module provides functions to save and load EvoNet networks
+to and from human-readable YAML files (default) or JSON files.
+The serialization preserves the full network topology:
+- Layers (index, role, label)
+- Neurons (id, activation, bias, role, label)
+- Connections (src, dst, weight, recurrent)
+
+YAML is recommended for readability and manual editing.
+JSON is provided as a secondary option for interoperability.
+"""
+
+from __future__ import annotations
+
+import json
+from typing import Any
+
+import yaml
+
+from evonet.core import Neuron, Nnet
+from evonet.enums import ConnectionType, NeuronRole
+
+# ---------------------------------------------------------------------------
+# Helper
+# ---------------------------------------------------------------------------
+
+
+def to_dict(net: Nnet) -> dict[str, Any]:
+    """
+    Convert an EvoNet network into a serializable dictionary.
+
+    Args:
+        net (Nnet): The network to convert.
+
+    Returns:
+        dict[str, Any]: A nested dictionary representation.
+    """
+    return {
+        "layers": [
+            {
+                "index": i,
+                "neurons": [
+                    {
+                        "id": n.id,
+                        "activation": n.activation_name,
+                        "bias": n.bias,
+                        "role": n.role.name,
+                        "label": n.label,
+                        "incoming": [
+                            {
+                                "source": c.source.id,
+                                "target": c.target.id,
+                                "weight": c.weight,
+                                "type": c.type.name,  # store enum as string
+                            }
+                            for c in n.incoming
+                        ],
+                    }
+                    for n in layer.neurons
+                ],
+            }
+            for i, layer in enumerate(net.layers)
+        ]
+    }
+
+
+def from_dict(data: dict[str, Any]) -> Nnet:
+    """Reconstruct a network from a dictionary created by `to_dict`."""
+    net = Nnet()
+    neuron_map: dict[str, Neuron] = {}
+
+    # Rebuild layers and neurons
+    for layer_info in data["layers"]:
+        net.add_layer()
+        for n_info in layer_info["neurons"]:
+            n = net.add_neuron(
+                activation=n_info["activation"],
+                bias=n_info["bias"],
+                role=NeuronRole[n_info["role"]],
+                label=n_info.get("label", ""),
+                connection_init="none",
+            )[0]
+            n.id = n_info["id"]
+            neuron_map[n.id] = n
+
+    # Rebuild connections
+    for layer_info in data["layers"]:
+        for n_info in layer_info["neurons"]:
+            for c_info in n_info["incoming"]:
+                src = neuron_map[c_info["source"]]
+                dst = neuron_map[c_info["target"]]
+                net.add_connection(
+                    src,
+                    dst,
+                    weight=c_info["weight"],
+                    conn_type=ConnectionType[c_info["type"]],
+                )
+
+    return net
+
+
+# ---------------------------------------------------------------------------
+# YAML interface
+# ---------------------------------------------------------------------------
+
+
+def save_yaml(net: Nnet, path: str) -> None:
+    """
+    Save a network to a YAML file (human-readable).
+
+    Args:
+        net (Nnet): The network to save.
+        path (str): Output file path.
+    """
+    with open(path, "w", encoding="utf-8") as f:
+        yaml.safe_dump(
+            to_dict(net),
+            f,
+            sort_keys=False,  # preserve order for readability
+            default_flow_style=False,  # block style (YAML best practice)
+        )
+
+
+def load_yaml(path: str) -> Nnet:
+    """
+    Load a network from a YAML file.
+
+    Args:
+        path (str): Path to the YAML file.
+
+    Returns:
+        Nnet: Reconstructed network.
+    """
+    with open(path, "r", encoding="utf-8") as f:
+        data = yaml.safe_load(f)
+    return from_dict(data)
+
+
+# ---------------------------------------------------------------------------
+# JSON interface
+# ---------------------------------------------------------------------------
+
+
+def save_json(net: Nnet, path: str) -> None:
+    """
+    Save a network to a JSON file.
+
+    Args:
+        net (Nnet): The network to save.
+        path (str): Output file path.
+    """
+    with open(path, "w", encoding="utf-8") as f:
+        json.dump(to_dict(net), f, indent=2)
+
+
+def load_json(path: str) -> Nnet:
+    """
+    Load a network from a JSON file.
+
+    Args:
+        path (str): Path to the JSON file.
+
+    Returns:
+        Nnet: Reconstructed network.
+    """
+    with open(path, "r", encoding="utf-8") as f:
+        data = json.load(f)
+    return from_dict(data)

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/evonet.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: evonet
-Version: 0.1.0.dev8
+Version: 0.1.0.dev10
 Summary: Evolvable neural network core for integration with EvoLib
 Author-email: EvoLib <evolib@dismail.de>
 License: MIT License
@@ -39,6 +39,7 @@ Requires-Dist: pyyaml>=6.0
 Requires-Dist: pandas>=2.3.0
 Requires-Dist: pydantic<3.0,>=2.7
 Requires-Dist: graphviz>=0.20.1
+Requires-Dist: matplotlib
 Provides-Extra: dev
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: types-PyYAML; extra == "dev"

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/evonet.egg-info/SOURCES.txt

@@ -6,11 +6,13 @@ evonet/__init__.py
 evonet/activation.py
 evonet/connection.py
 evonet/core.py
+evonet/core_mit_plot_simple.py
 evonet/enums.py
 evonet/io.py
 evonet/layer.py
 evonet/mutation.py
 evonet/neuron.py
+evonet/serialization.py
 evonet/utils.py
 evonet/visualize.py
 evonet.egg-info/PKG-INFO

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/evonet.egg-info/requires.txt

@@ -3,6 +3,7 @@ pyyaml>=6.0
 pandas>=2.3.0
 pydantic<3.0,>=2.7
 graphviz>=0.20.1
+matplotlib
 
 [dev]
 mypy

{evonet-0.1.0.dev8 → evonet-0.1.0.dev10}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "evonet"
-version = "0.1.0.dev8"
+version = "0.1.0.dev10"
 description = "Evolvable neural network core for integration with EvoLib"
 authors = [
     { name = "EvoLib", email = "evolib@dismail.de" }
@@ -17,7 +17,8 @@ dependencies = [
     "pyyaml >=6.0",
     "pandas >=2.3.0",
     "pydantic >= 2.7,<3.0",
-    "graphviz>=0.20.1"
+    "graphviz>=0.20.1",
+    "matplotlib"
 ]
 
 classifiers = [