Update docs and setup.py to reflect current implementation.

Author: CodeReclaimers

docs/conf.py

@@ -42,13 +42,13 @@
     'sphinx.ext.inheritance_diagram', 
 ]
 
-extlinks = {'pytypes': ('https://docs.python.org/3.5/library/stdtypes.html#%s',
+extlinks = {'pytypes': ('https://docs.python.org/3/library/stdtypes.html#%s',
                         None),
-            'pygloss': ('https://docs.python.org/3.5/glossary.html#term-%s',
+            'pygloss': ('https://docs.python.org/3/glossary.html#term-%s',
                         None),
-            'datamodel': ('https://docs.python.org/3.5/reference/datamodel.html#%s',
+            'datamodel': ('https://docs.python.org/3/reference/datamodel.html#%s',
                           None),
-            'pylib': ('https://docs.python.org/3.5/library/%s',
+            'pylib': ('https://docs.python.org/3/library/%s',
                       None)}
 
 # Add any paths that contain templates here, relative to this directory.
@@ -67,17 +67,17 @@
 
 # General information about the project.
 project = u'NEAT-Python'
-copyright = u'2015-2019, CodeReclaimers, LLC'
+copyright = u'2015-2025, CodeReclaimers, LLC'
 author = u'CodeReclaimers, LLC'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.92'
+version = '1.0.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.92'
+release = '1.0.0'
 
 if version != release:
     tags.add('draft')
@@ -129,8 +129,8 @@
 else:
     todo_include_todos = False
 
-# Provide links to python3.5 documentation
-intersphinx_mapping = {'python': ('https://docs.python.org/3.5', None)}
+# Provide links to python3 documentation
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
 
 # -- Options for HTML output ----------------------------------------------
 

docs/glossary.rst

@@ -23,8 +23,7 @@ Glossary
     Also known as a neuron (as in a *neural* network). They are of three types:
     :term:`input <input node>`, :term:`hidden <hidden node>`, and :term:`output <output node>`. Nodes have one or more :term:`attributes`, such
     as an :term:`activation function`; all are determined by their :term:`gene`. Classes of node genes include :py:class:`genes.DefaultNodeGene` and
-    :py:class:`iznn.IZNodeGene`. (They should not be confused with :term:`compute nodes <compute node>`, host machines on which :py:mod:`distributed`
-    evaluations of :term:`genomes <genome>` are performed.)
+    :py:class:`iznn.IZNodeGene`.
 
   input node
     These are the :term:`nodes <node>` through which the network receives inputs. They cannot be deleted (although :term:`connections <connection>`
@@ -140,20 +139,4 @@ Glossary
     check if a/the termination criterion is satisfied; if not, repeat. (The ordering in the :py:mod:`population` module is somewhat different.)
     Generations are numbered, and a limit on the number of generations is one type of termination criterion.
 
-  compute node
-    Using the :py:mod:`distributed` module, genomes can be evaluated on multiple machines (including virtual machines) at once. Each such
-    machine/host is called a ``compute node``. These are of two types, :term:`primary nodes <primary node>` and
-    :term:`secondary nodes <secondary node>`.
-
-  primary node
-  primary compute node
-    If using the :py:mod:`distributed` module, you will need one primary :term:`compute node` and at least one :term:`secondary node`. The primary node
-    creates and mutates genomes, then distributes them to the secondary nodes for evaluation. (It does not do any evaluations itself; thus, at least
-    one secondary node is required.)
-
-  secondary node
-  secondary compute node
-    If using the :py:mod:`distributed` module, you will need at least one secondary :term:`compute node`, as well as a :term:`primary node`. The secondary
-    nodes evaluate genomes, distributed to them by the primary node.
-
 :ref:`Table of Contents <toc-label>`

docs/index.rst

@@ -4,7 +4,7 @@ Welcome to NEAT-Python's documentation!
 :abbr:`NEAT (NeuroEvolution of Augmenting Topologies)` is a method developed by Kenneth O. Stanley for evolving arbitrary neural
 networks. NEAT-Python is a pure Python implementation of NEAT, with no dependencies other than the Python standard library.
 
-Currently this library supports Python versions 3.6 through 3.11, as well as PyPy 3.
+Currently this library supports Python versions 3.8 through 3.14, as well as PyPy 3.
 
 Many thanks to the original authors of this implementation, Cesar Gomes Miguel, Carolina Feher da Silva, and Marcio Lobo Netto!
 

docs/installation.rst

@@ -11,16 +11,16 @@ two methods outlined below:
 
 Install neat-python from PyPI using pip
 ---------------------------------------
-To install the most recent release (version 0.92) from PyPI, you should run the command (as root or using `sudo`
+To install the most recent release (version 1.0.0) from PyPI, you should run the command (as root or using `sudo`
 as necessary)::
 
     pip install neat-python
 
 Note that the examples are not included with the package installed from PyPI, so you should download the `source archive
-for release 0.92
-<https://github.com/CodeReclaimers/neat-python/releases/tag/v0.92>`_ and use the example code contained in it.
+for release 1.0.0
+<https://github.com/CodeReclaimers/neat-python/releases/tag/v1.0.0>`_ and use the example code contained in it.
 
-You may also just get the 0.92 release source, and install it directly using `setup.py` (as shown below)
+You may also just get the 1.0.0 release source, and install it directly using `setup.py` (as shown below)
 instead of `pip`.
 
 Install neat-python from source using setup.py
@@ -29,8 +29,8 @@ Obtain the source code by either cloning the source repository::
 
     git clone https://github.com/CodeReclaimers/neat-python.git
 
-or downloading the `source archive for release 0.92
-<https://github.com/CodeReclaimers/neat-python/releases/tag/v0.92>`_.
+or downloading the `source archive for release 1.0.0
+<https://github.com/CodeReclaimers/neat-python/releases/tag/v1.0.0>`_.
 
 Note that the most current code in the repository may not always be in the most polished state, but I do make sure the
 tests pass and that most of the examples run.  If you encounter any problems, please open an `issue on GitHub

docs/module_summaries.rst

@@ -1447,6 +1447,60 @@ See http://www.izhikevich.org/publications/spikes.pdf.
     .. versionchanged:: 0.92
       ``__gene_attributes__`` changed to ``_gene_attributes``, since it is not a Python internal variable. 
 
+.. py:module:: innovation
+   :synopsis: Tracks innovation numbers for structural mutations in NEAT.
+
+innovation
+----------
+Tracks innovation numbers for structural mutations in NEAT, as described in Stanley & Miikkulainen (2002).
+
+  .. index:: ! innovation number
+  .. index:: structural mutation
+
+  .. py:class:: InnovationTracker(start_number=0)
+
+    Tracks innovation numbers for structural mutations in NEAT. This class maintains a global counter that increments
+    across all generations and a generation-specific dictionary for deduplication of identical mutations within the
+    same generation.
+
+    Innovation numbers are assigned when:
+
+    - A new connection is added between two nodes
+    - A connection is split by adding a node (creates two new connections)
+    - Initial connections are created in the starting population
+
+    The tracker ensures that if multiple genomes independently make the same structural mutation in one generation,
+    they receive the same innovation number. This enables proper gene alignment during :term:`crossover`.
+
+    :param int start_number: The initial value for the global counter (default: 0). The first innovation will be start_number + 1.
+
+    .. versionadded:: 1.0
+
+    .. py:method:: get_innovation_number(input_node, output_node, mutation_type='add_connection')
+
+      Get or assign an innovation number for a structural mutation. If this exact mutation (same nodes and type)
+      has already occurred in the current generation, returns the existing innovation number. Otherwise, increments
+      the global counter and assigns a new innovation number.
+
+      :param int input_node: The input node ID for the connection
+      :param int output_node: The output node ID for the connection
+      :param str mutation_type: Type of mutation: ``'add_connection'`` (new connection), ``'add_node_in'`` (connection from original input to new node), ``'add_node_out'`` (connection from new node to original output), or ``'initial_connection'`` (connection in initial population)
+      :return: The innovation number for this structural mutation
+      :rtype: :pytypes:`int <typesnumeric>`
+
+    .. py:method:: reset_generation()
+
+      Clear generation-specific tracking at the start of a new generation. This method should be called at the
+      beginning of each generation's reproduction phase. It clears the generation_innovations dictionary but preserves
+      the global_counter so innovation numbers never repeat.
+
+    .. py:method:: get_current_innovation_number()
+
+      Get the current (most recently assigned) innovation number.
+
+      :return: The current value of the global counter
+      :rtype: :pytypes:`int <typesnumeric>`
+
 .. py:module:: math_util
    :synopsis: Contains some mathematical functions not found in the Python2 standard library, plus a mechanism for looking up some commonly used functions (such as for the species_fitness_func) by name.
 

docs/network_export.rst

@@ -1,7 +1,7 @@
 Network Export
 ==============
 
-.. versionadded:: 1.0.1
+.. versionadded:: 1.0
 
 NEAT-Python provides the ability to export trained neural networks to a framework-agnostic JSON format. This allows you to:
 

setup.py

@@ -28,6 +28,9 @@
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'Programming Language :: Python :: Implementation :: PyPy',
         'Topic :: Scientific/Engineering'
     ]