Merge branch 'EMI-Group:main' into main

.gitignore

@@ -116,4 +116,5 @@ cython_debug/
 *.pot
 *.mo
 
-tutorials/.ipynb_checkpoints/*
+tutorials/.ipynb_checkpoints/*
+docs/_build/*

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+     - method: pip
+       path: . 
+     - requirements: docs/requirements.txt

docs/conf.py

@@ -0,0 +1,40 @@
+import os
+import sys
+sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../src'))
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'TensorNEAT'
+copyright = '2025, Lishuang Wang'
+author = 'Lishuang Wang'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+]
+
+autodoc_mock_imports = [
+    "evox"
+]
+
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,18 @@
+.. TensorNEAT documentation master file, created by
+   sphinx-quickstart on Mon Feb 17 14:51:55 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+TensorNEAT documentation
+========================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   source/tensorneat
+
+.. .. automodule:: tensorneat
+..    :members:
+..    :undoc-members:
+..    :show-inheritance:

docs/requirements.txt

@@ -0,0 +1 @@
+sphinx_rtd_theme

docs/source/modules.rst

@@ -0,0 +1,7 @@
+tensorneat
+==========
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat

docs/source/tensorneat.algorithm.hyperneat.rst

@@ -0,0 +1,37 @@
+tensorneat.algorithm.hyperneat package
+======================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.algorithm.hyperneat.substrate
+
+Submodules
+----------
+
+tensorneat.algorithm.hyperneat.hyperneat module
+-----------------------------------------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.hyperneat
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.algorithm.hyperneat.hyperneat\_feedforward module
+------------------------------------------------------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.hyperneat_feedforward
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.algorithm.hyperneat
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.algorithm.hyperneat.substrate.rst

@@ -0,0 +1,45 @@
+tensorneat.algorithm.hyperneat.substrate package
+================================================
+
+Submodules
+----------
+
+tensorneat.algorithm.hyperneat.substrate.base module
+----------------------------------------------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.substrate.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.algorithm.hyperneat.substrate.default module
+-------------------------------------------------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.substrate.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.algorithm.hyperneat.substrate.full module
+----------------------------------------------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.substrate.full
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.algorithm.hyperneat.substrate.mlp module
+---------------------------------------------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.substrate.mlp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.algorithm.hyperneat.substrate
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.algorithm.neat.rst

@@ -0,0 +1,29 @@
+tensorneat.algorithm.neat package
+=================================
+
+Submodules
+----------
+
+tensorneat.algorithm.neat.neat module
+-------------------------------------
+
+.. automodule:: tensorneat.algorithm.neat.neat
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.algorithm.neat.species module
+----------------------------------------
+
+.. automodule:: tensorneat.algorithm.neat.species
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.algorithm.neat
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.algorithm.rst

@@ -0,0 +1,30 @@
+tensorneat.algorithm package
+============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.algorithm.hyperneat
+   tensorneat.algorithm.neat
+
+Submodules
+----------
+
+tensorneat.algorithm.base module
+--------------------------------
+
+.. automodule:: tensorneat.algorithm.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.algorithm
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.common.evox_adaptors.rst

@@ -0,0 +1,29 @@
+tensorneat.common.evox\_adaptors package
+========================================
+
+Submodules
+----------
+
+tensorneat.common.evox\_adaptors.algorithm\_adaptor module
+----------------------------------------------------------
+
+.. automodule:: tensorneat.common.evox_adaptors.algorithm_adaptor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.evox\_adaptors.tensorneat\_monitor module
+-----------------------------------------------------------
+
+.. automodule:: tensorneat.common.evox_adaptors.tensorneat_monitor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.common.evox_adaptors
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.common.functions.rst

@@ -0,0 +1,53 @@
+tensorneat.common.functions package
+===================================
+
+Submodules
+----------
+
+tensorneat.common.functions.act\_jnp module
+-------------------------------------------
+
+.. automodule:: tensorneat.common.functions.act_jnp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.functions.act\_sympy module
+---------------------------------------------
+
+.. automodule:: tensorneat.common.functions.act_sympy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.functions.agg\_jnp module
+-------------------------------------------
+
+.. automodule:: tensorneat.common.functions.agg_jnp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.functions.agg\_sympy module
+---------------------------------------------
+
+.. automodule:: tensorneat.common.functions.agg_sympy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.functions.manager module
+------------------------------------------
+
+.. automodule:: tensorneat.common.functions.manager
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.common.functions
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.common.rst

@@ -0,0 +1,62 @@
+tensorneat.common package
+=========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.common.evox_adaptors
+   tensorneat.common.functions
+
+Submodules
+----------
+
+tensorneat.common.graph module
+------------------------------
+
+.. automodule:: tensorneat.common.graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.state module
+------------------------------
+
+.. automodule:: tensorneat.common.state
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.stateful\_class module
+----------------------------------------
+
+.. automodule:: tensorneat.common.stateful_class
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.sympy\_tools module
+-------------------------------------
+
+.. automodule:: tensorneat.common.sympy_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.common.tools module
+------------------------------
+
+.. automodule:: tensorneat.common.tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.common
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.gene.conn.rst

@@ -0,0 +1,37 @@
+tensorneat.genome.gene.conn package
+===================================
+
+Submodules
+----------
+
+tensorneat.genome.gene.conn.base module
+---------------------------------------
+
+.. automodule:: tensorneat.genome.gene.conn.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.gene.conn.default module
+------------------------------------------
+
+.. automodule:: tensorneat.genome.gene.conn.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.gene.conn.origin module
+-----------------------------------------
+
+.. automodule:: tensorneat.genome.gene.conn.origin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.gene.conn
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.gene.node.rst

@@ -0,0 +1,45 @@
+tensorneat.genome.gene.node package
+===================================
+
+Submodules
+----------
+
+tensorneat.genome.gene.node.base module
+---------------------------------------
+
+.. automodule:: tensorneat.genome.gene.node.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.gene.node.bias module
+---------------------------------------
+
+.. automodule:: tensorneat.genome.gene.node.bias
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.gene.node.default module
+------------------------------------------
+
+.. automodule:: tensorneat.genome.gene.node.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.gene.node.origin module
+-----------------------------------------
+
+.. automodule:: tensorneat.genome.gene.node.origin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.gene.node
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.gene.rst

@@ -0,0 +1,30 @@
+tensorneat.genome.gene package
+==============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.genome.gene.conn
+   tensorneat.genome.gene.node
+
+Submodules
+----------
+
+tensorneat.genome.gene.base module
+----------------------------------
+
+.. automodule:: tensorneat.genome.gene.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.gene
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.operations.crossover.rst

@@ -0,0 +1,29 @@
+tensorneat.genome.operations.crossover package
+==============================================
+
+Submodules
+----------
+
+tensorneat.genome.operations.crossover.base module
+--------------------------------------------------
+
+.. automodule:: tensorneat.genome.operations.crossover.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.operations.crossover.default module
+-----------------------------------------------------
+
+.. automodule:: tensorneat.genome.operations.crossover.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.operations.crossover
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.operations.distance.rst

@@ -0,0 +1,29 @@
+tensorneat.genome.operations.distance package
+=============================================
+
+Submodules
+----------
+
+tensorneat.genome.operations.distance.base module
+-------------------------------------------------
+
+.. automodule:: tensorneat.genome.operations.distance.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.operations.distance.default module
+----------------------------------------------------
+
+.. automodule:: tensorneat.genome.operations.distance.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.operations.distance
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.operations.mutation.rst

@@ -0,0 +1,29 @@
+tensorneat.genome.operations.mutation package
+=============================================
+
+Submodules
+----------
+
+tensorneat.genome.operations.mutation.base module
+-------------------------------------------------
+
+.. automodule:: tensorneat.genome.operations.mutation.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.operations.mutation.default module
+----------------------------------------------------
+
+.. automodule:: tensorneat.genome.operations.mutation.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.operations.mutation
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.operations.rst

@@ -0,0 +1,20 @@
+tensorneat.genome.operations package
+====================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.genome.operations.crossover
+   tensorneat.genome.operations.distance
+   tensorneat.genome.operations.mutation
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome.operations
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.genome.rst

@@ -0,0 +1,54 @@
+tensorneat.genome package
+=========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.genome.gene
+   tensorneat.genome.operations
+
+Submodules
+----------
+
+tensorneat.genome.base module
+-----------------------------
+
+.. automodule:: tensorneat.genome.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.default module
+--------------------------------
+
+.. automodule:: tensorneat.genome.default
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.recurrent module
+----------------------------------
+
+.. automodule:: tensorneat.genome.recurrent
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.genome.utils module
+------------------------------
+
+.. automodule:: tensorneat.genome.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.genome
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.problem.func_fit.rst

@@ -0,0 +1,45 @@
+tensorneat.problem.func\_fit package
+====================================
+
+Submodules
+----------
+
+tensorneat.problem.func\_fit.custom module
+------------------------------------------
+
+.. automodule:: tensorneat.problem.func_fit.custom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.problem.func\_fit.func\_fit module
+---------------------------------------------
+
+.. automodule:: tensorneat.problem.func_fit.func_fit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.problem.func\_fit.xor module
+---------------------------------------
+
+.. automodule:: tensorneat.problem.func_fit.xor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.problem.func\_fit.xor3d module
+-----------------------------------------
+
+.. automodule:: tensorneat.problem.func_fit.xor3d
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.problem.func_fit
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.problem.rl.rst

@@ -0,0 +1,37 @@
+tensorneat.problem.rl package
+=============================
+
+Submodules
+----------
+
+tensorneat.problem.rl.brax module
+---------------------------------
+
+.. automodule:: tensorneat.problem.rl.brax
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.problem.rl.gymnax module
+-----------------------------------
+
+.. automodule:: tensorneat.problem.rl.gymnax
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tensorneat.problem.rl.rl\_jit module
+------------------------------------
+
+.. automodule:: tensorneat.problem.rl.rl_jit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.problem.rl
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.problem.rst

@@ -0,0 +1,30 @@
+tensorneat.problem package
+==========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.problem.func_fit
+   tensorneat.problem.rl
+
+Submodules
+----------
+
+tensorneat.problem.base module
+------------------------------
+
+.. automodule:: tensorneat.problem.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat.problem
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tensorneat.rst

@@ -0,0 +1,32 @@
+tensorneat package
+==================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tensorneat.algorithm
+   tensorneat.common
+   tensorneat.genome
+   tensorneat.problem
+
+Submodules
+----------
+
+tensorneat.pipeline module
+--------------------------
+
+.. automodule:: tensorneat.pipeline
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tensorneat
+   :members:
+   :undoc-members:
+   :show-inheritance:

src/tensorneat/__init__.py

@@ -0,0 +1,4 @@
+__all__ = ["algorithm", "common", "genome", "problem"]
+
+from . import algorithm, common, genome, problem
+from .pipeline import Pipeline