From 4791a1736292d4d61e84eac523834fd37bceced2 Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 16:10:20 +0800 Subject: [PATCH 1/9] add readthedocs support --- .gitignore | 3 +- .readthedocs.yaml | 23 +++++++ docs/Makefile | 20 ++++++ docs/conf.py | 35 +++++++++++ docs/index.rst | 13 ++++ docs/make.bat | 35 +++++++++++ docs/source/modules.rst | 7 +++ .../source/tensorneat.algorithm.hyperneat.rst | 37 +++++++++++ ...nsorneat.algorithm.hyperneat.substrate.rst | 45 ++++++++++++++ docs/source/tensorneat.algorithm.neat.rst | 29 +++++++++ docs/source/tensorneat.algorithm.rst | 30 +++++++++ .../tensorneat.common.evox_adaptors.rst | 29 +++++++++ docs/source/tensorneat.common.functions.rst | 53 ++++++++++++++++ docs/source/tensorneat.common.rst | 62 +++++++++++++++++++ docs/source/tensorneat.genome.gene.conn.rst | 37 +++++++++++ docs/source/tensorneat.genome.gene.node.rst | 45 ++++++++++++++ docs/source/tensorneat.genome.gene.rst | 30 +++++++++ ...tensorneat.genome.operations.crossover.rst | 29 +++++++++ .../tensorneat.genome.operations.distance.rst | 29 +++++++++ .../tensorneat.genome.operations.mutation.rst | 29 +++++++++ docs/source/tensorneat.genome.operations.rst | 20 ++++++ docs/source/tensorneat.genome.rst | 54 ++++++++++++++++ docs/source/tensorneat.problem.func_fit.rst | 45 ++++++++++++++ docs/source/tensorneat.problem.rl.rst | 37 +++++++++++ docs/source/tensorneat.problem.rst | 30 +++++++++ docs/source/tensorneat.rst | 32 ++++++++++ src/tensorneat/__init__.py | 4 ++ 27 files changed, 841 insertions(+), 1 deletion(-) create mode 100644 .readthedocs.yaml create mode 100644 docs/Makefile create mode 100644 docs/conf.py create mode 100644 docs/index.rst create mode 100644 docs/make.bat create mode 100644 docs/source/modules.rst create mode 100644 docs/source/tensorneat.algorithm.hyperneat.rst create mode 100644 docs/source/tensorneat.algorithm.hyperneat.substrate.rst create mode 100644 docs/source/tensorneat.algorithm.neat.rst create mode 100644 docs/source/tensorneat.algorithm.rst create mode 100644 docs/source/tensorneat.common.evox_adaptors.rst create mode 100644 docs/source/tensorneat.common.functions.rst create mode 100644 docs/source/tensorneat.common.rst create mode 100644 docs/source/tensorneat.genome.gene.conn.rst create mode 100644 docs/source/tensorneat.genome.gene.node.rst create mode 100644 docs/source/tensorneat.genome.gene.rst create mode 100644 docs/source/tensorneat.genome.operations.crossover.rst create mode 100644 docs/source/tensorneat.genome.operations.distance.rst create mode 100644 docs/source/tensorneat.genome.operations.mutation.rst create mode 100644 docs/source/tensorneat.genome.operations.rst create mode 100644 docs/source/tensorneat.genome.rst create mode 100644 docs/source/tensorneat.problem.func_fit.rst create mode 100644 docs/source/tensorneat.problem.rl.rst create mode 100644 docs/source/tensorneat.problem.rst create mode 100644 docs/source/tensorneat.rst create mode 100644 src/tensorneat/__init__.py diff --git a/.gitignore b/.gitignore index 30e1f6a..28be23c 100644 --- a/.gitignore +++ b/.gitignore @@ -116,4 +116,5 @@ cython_debug/ *.pot *.mo -tutorials/.ipynb_checkpoints/* \ No newline at end of file +tutorials/.ipynb_checkpoints/* +docs/_build/* diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..719194c --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,23 @@ +# 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: +# - requirements: docs/requirements.txt + \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..166679f --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,35 @@ +import os +import sys +script_dir = os.path.dirname(os.path.abspath(__file__)) +sys.path.insert(0, os.path.join(script_dir, '..', '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', +] + +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'] diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..ad84d9d --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,13 @@ +.. 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 \ No newline at end of file diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..32bb245 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/modules.rst b/docs/source/modules.rst new file mode 100644 index 0000000..bda3bfc --- /dev/null +++ b/docs/source/modules.rst @@ -0,0 +1,7 @@ +src +=== + +.. toctree:: + :maxdepth: 4 + + tensorneat diff --git a/docs/source/tensorneat.algorithm.hyperneat.rst b/docs/source/tensorneat.algorithm.hyperneat.rst new file mode 100644 index 0000000..c327d51 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.algorithm.hyperneat.substrate.rst b/docs/source/tensorneat.algorithm.hyperneat.substrate.rst new file mode 100644 index 0000000..3820998 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.algorithm.neat.rst b/docs/source/tensorneat.algorithm.neat.rst new file mode 100644 index 0000000..d80590e --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.algorithm.rst b/docs/source/tensorneat.algorithm.rst new file mode 100644 index 0000000..f43e3bd --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.common.evox_adaptors.rst b/docs/source/tensorneat.common.evox_adaptors.rst new file mode 100644 index 0000000..3f9ffd2 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.common.functions.rst b/docs/source/tensorneat.common.functions.rst new file mode 100644 index 0000000..3cd64b9 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.common.rst b/docs/source/tensorneat.common.rst new file mode 100644 index 0000000..551ffcf --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.gene.conn.rst b/docs/source/tensorneat.genome.gene.conn.rst new file mode 100644 index 0000000..db0b127 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.gene.node.rst b/docs/source/tensorneat.genome.gene.node.rst new file mode 100644 index 0000000..e4de09b --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.gene.rst b/docs/source/tensorneat.genome.gene.rst new file mode 100644 index 0000000..cda1af8 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.operations.crossover.rst b/docs/source/tensorneat.genome.operations.crossover.rst new file mode 100644 index 0000000..2b93128 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.operations.distance.rst b/docs/source/tensorneat.genome.operations.distance.rst new file mode 100644 index 0000000..889ce7c --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.operations.mutation.rst b/docs/source/tensorneat.genome.operations.mutation.rst new file mode 100644 index 0000000..c85698b --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.operations.rst b/docs/source/tensorneat.genome.operations.rst new file mode 100644 index 0000000..de56434 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.genome.rst b/docs/source/tensorneat.genome.rst new file mode 100644 index 0000000..a870a78 --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.problem.func_fit.rst b/docs/source/tensorneat.problem.func_fit.rst new file mode 100644 index 0000000..a35782d --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.problem.rl.rst b/docs/source/tensorneat.problem.rl.rst new file mode 100644 index 0000000..189f4dd --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.problem.rst b/docs/source/tensorneat.problem.rst new file mode 100644 index 0000000..c1fb86b --- /dev/null +++ b/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: diff --git a/docs/source/tensorneat.rst b/docs/source/tensorneat.rst new file mode 100644 index 0000000..a852868 --- /dev/null +++ b/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: diff --git a/src/tensorneat/__init__.py b/src/tensorneat/__init__.py new file mode 100644 index 0000000..0380fcf --- /dev/null +++ b/src/tensorneat/__init__.py @@ -0,0 +1,4 @@ +__all__ = ["algorithm", "common", "genome", "problem"] + +from . import algorithm, common, genome, problem +from .pipeline import Pipeline \ No newline at end of file From 5424249918b2424617edcc51e652f55e52e4e730 Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 16:13:37 +0800 Subject: [PATCH 2/9] update readthedocs config --- .readthedocs.yaml | 6 +++--- docs/requirements.txt | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) create mode 100644 docs/requirements.txt diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 719194c..32cd869 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -17,7 +17,7 @@ sphinx: # 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: -# - requirements: docs/requirements.txt +python: + install: + - requirements: docs/requirements.txt \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..52b04f2 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +sphinx_rtd_theme \ No newline at end of file From 7e717853f31fa7de9937f4c7eda71f7a04c0ff12 Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 16:24:19 +0800 Subject: [PATCH 3/9] add link to source code function in docs --- docs/index.rst | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index ad84d9d..32cb4e9 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -10,4 +10,9 @@ TensorNEAT documentation :maxdepth: 2 :caption: Contents: - source/tensorneat \ No newline at end of file + source/tensorneat + +.. automodule:: tensorneat + :members: + :undoc-members: + :show-inheritance: From 5ec163ccc0e5ece5042ffc3d9a5130eb8a5545ff Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 16:36:57 +0800 Subject: [PATCH 4/9] update document --- .readthedocs.yaml | 5 ++++- docs/requirements.txt | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 32cd869..8a94b6f 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,6 +9,8 @@ build: os: ubuntu-22.04 tools: python: "3.10" + commands: + - sphinx-apidoc -o docs/source src/tensorneat # Build documentation in the "docs/" directory with Sphinx sphinx: @@ -20,4 +22,5 @@ sphinx: python: install: - requirements: docs/requirements.txt - \ No newline at end of file + + diff --git a/docs/requirements.txt b/docs/requirements.txt index 52b04f2..b5bb3b1 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1 +1,2 @@ +sphinx-apidoc sphinx_rtd_theme \ No newline at end of file From 185b7162ec7c91dc2f66e34a8819965afb593b1f Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 17:07:14 +0800 Subject: [PATCH 5/9] update doc --- .readthedocs.yaml | 2 -- docs/Makefile | 20 -------------------- docs/make.bat | 35 ----------------------------------- docs/source/modules.rst | 4 ++-- 4 files changed, 2 insertions(+), 59 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/make.bat diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 8a94b6f..316f855 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,8 +9,6 @@ build: os: ubuntu-22.04 tools: python: "3.10" - commands: - - sphinx-apidoc -o docs/source src/tensorneat # Build documentation in the "docs/" directory with Sphinx sphinx: diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index d4bb2cb..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 32bb245..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -if "%1" == "" goto help - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/docs/source/modules.rst b/docs/source/modules.rst index bda3bfc..c41cabf 100644 --- a/docs/source/modules.rst +++ b/docs/source/modules.rst @@ -1,5 +1,5 @@ -src -=== +tensorneat +========== .. toctree:: :maxdepth: 4 From b3277d1b9d4927fc38954c3a8d28eb8d10199fc5 Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 17:09:59 +0800 Subject: [PATCH 6/9] remove useless requirement --- docs/requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index b5bb3b1..52b04f2 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,2 +1 @@ -sphinx-apidoc sphinx_rtd_theme \ No newline at end of file From 72c1604ea0e7e908ca07ebf5878b0f2b1b9583a5 Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 17:12:22 +0800 Subject: [PATCH 7/9] upodate conf.py in doc --- docs/conf.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 166679f..715a917 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,7 +1,6 @@ import os import sys -script_dir = os.path.dirname(os.path.abspath(__file__)) -sys.path.insert(0, os.path.join(script_dir, '..', 'src')) +sys.path.insert(0, os.path.abspath('../src')) # Configuration file for the Sphinx documentation builder. # From 8e240b20c67b4f014008883b59bbfa5b5607f7ef Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 17:25:59 +0800 Subject: [PATCH 8/9] update doc --- .readthedocs.yaml | 6 +++--- docs/conf.py | 1 + docs/index.rst | 8 ++++---- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 316f855..3f8c618 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -19,6 +19,6 @@ sphinx: # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: install: - - requirements: docs/requirements.txt - - + - method: pip + path: . + - requirements: docs/requirements.txt \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 715a917..1eed2b2 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,6 @@ 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. diff --git a/docs/index.rst b/docs/index.rst index 32cb4e9..21bdf42 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -12,7 +12,7 @@ TensorNEAT documentation source/tensorneat -.. automodule:: tensorneat - :members: - :undoc-members: - :show-inheritance: +.. .. automodule:: tensorneat +.. :members: +.. :undoc-members: +.. :show-inheritance: From d787e13a724e78f26c2877455b6c549dd95635ad Mon Sep 17 00:00:00 2001 From: wls2002 Date: Mon, 17 Feb 2025 17:30:33 +0800 Subject: [PATCH 9/9] update doc --- docs/conf.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index 1eed2b2..856c1fa 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -24,6 +24,11 @@ extensions = [ 'sphinx.ext.viewcode', ] +autodoc_mock_imports = [ + "evox" +] + + templates_path = ['_templates'] exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']