From 85edb8abfc16093f8601923c395de62c7660f921 Mon Sep 17 00:00:00 2001 From: iantbeck Date: Fri, 3 May 2024 10:50:55 -0400 Subject: [PATCH] stage docs --- docs/Makefile | 8 +- docs/README.md | 15 --- docs/requirements.yml | 2 +- docs/source/conf.py | 207 +++--------------------------------------- docs/source/index.rst | 29 +++++- 5 files changed, 40 insertions(+), 221 deletions(-) delete mode 100644 docs/README.md diff --git a/docs/Makefile b/docs/Makefile index 8883c11..d0c3cbf 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,10 +1,10 @@ # Minimal makefile for Sphinx documentation # -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SPHINXPROJ = PESLearn +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build SOURCEDIR = source BUILDDIR = build diff --git a/docs/README.md b/docs/README.md deleted file mode 100644 index a090ac7..0000000 --- a/docs/README.md +++ /dev/null @@ -1,15 +0,0 @@ -# Compiling PESLearn's Documentation - -The docs for this project are built with Sphinx. To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed. - -``` -conda install sphinx sphinx_rtd_theme -``` - -Once installed, you can use the Makefile in this directory to compile static HTML pages by - -``` -make html -``` - -The compiled docs will be in the _build directory and can be viewed by opening index.html (which may itself be inside a directory called html/ depending on what version of Sphinx is installed). diff --git a/docs/requirements.yml b/docs/requirements.yml index c688140..24f48e0 100644 --- a/docs/requirements.yml +++ b/docs/requirements.yml @@ -3,7 +3,7 @@ channels: - nodefaults - conda-forge dependencies: - - python=3 + - python=3.8 - sphinx - sphinx_rtd_theme - sphinx-automodapi diff --git a/docs/source/conf.py b/docs/source/conf.py index 87ada1a..e7aed5f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -1,213 +1,28 @@ -# -*- coding: utf-8 -*- -# # Configuration file for the Sphinx documentation builder. # -# This file does only contain a selection of the most common options. For a -# full list see the documentation: -# http://www.sphinx-doc.org/en/master/config - -import datetime -import os -import sys - -sys.path.insert(0, os.path.abspath('../..')) -import peslearn - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - +# 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 = 'PESLearn' -copyright = f'{datetime.datetime.today().year}' -author = 'The PESLearn Development Team' - -# The short X.Y version -version = peslearn.__version__ -# The full version, including alpha/beta/rc tags -release = peslearn.__version__ - +project = 'PES-Learn' +copyright = '2024, PES-Learn Development Team' +author = 'PES-Learn Development Team' +release = '1.0.0' # -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.intersphinx', - 'sphinx.ext.doctest', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.viewcode', - 'sphinx.ext.extlinks', - 'sphinx.ext.graphviz', - 'sphinx.ext.autosummary', - 'sphinx.ext.napoleon', - 'sphinx_automodapi.automodapi', - 'sphinx_automodapi.automodsumm', - 'sphinx_automodapi.smart_resolver', - "sphinx_autodoc_typehints", - "sphinxcontrib.autodoc_pydantic", -] - -autosummary_generate = True -automodapi_toctreedirnm = 'api' -autodoc_typehints = "description" -napoleon_use_param = True -napoleon_use_rtype = True -autodoc_pydantic_model_hide_paramlist = True -autodoc_pydantic_model_show_config_summary = False -autodoc_pydantic_field_swap_name_and_alias = True +extensions = [] -# Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = "en" - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path . exclude_patterns = [] -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'default' # -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'sphinx_rtd_theme' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". +html_theme = 'alabaster' html_static_path = ['_static'] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# The default sidebars (for documents that don't match any pattern) are -# defined by theme itself. Builtin themes are using these templates by -# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', -# 'searchbox.html']``. -# -# html_sidebars = {} - - -# -- Options for HTMLHelp output --------------------------------------------- - -# Output file base name for HTML help builder. -htmlhelp_basename = 'PESLearndoc' - - -# -- Options for LaTeX output ------------------------------------------------ - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'PESLearn.tex', 'PESLearn Documentation', - 'The PESLearn Development Team', 'manual'), -] - - -# -- Options for manual page output ------------------------------------------ - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'peslearn', 'PESLearn Documentation', - [author], 1) -] - - -# -- Options for Texinfo output ---------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'PESLearn', 'PESLearn Documentation', - author, 'PESLearn', 'One line description of project.', - 'Miscellaneous'), -] - - -# -- Extension configuration ------------------------------------------------- - -extlinks = { - 'issue': ('https://github.com/CCQC/PES-Learn/issue/%s', 'GH#%s'), - 'pr': ('https://github.com/CCQC/PES-Learn/pull/%s', 'GH#%s') -} - -# -- Options for intersphinx extension --------------------------------------- - -# Example configuration for intersphinx: refer to the Python standard library. -""" -intersphinx_mapping = {'python': ('https://docs.python.org/3.10', None), - "numpy": ("https://numpy.org/doc/stable/", None), - 'scipy': ('https://docs.scipy.org/doc/scipy/', None), - 'matplotlib': ('https://matplotlib.org/stable/', None), - "qcelemental": ("http://docs.qcarchive.molssi.org/projects/QCElemental/en/latest/", None), - "qcportal": ("http://docs.qcarchive.molssi.org/projects/QCPortal/en/latest/", None), - "qcfractal": ("http://docs.qcarchive.molssi.org/projects/QCFractal/en/latest/", None), - } -""" -# -- Options for todo extension ---------------------------------------------- - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = True diff --git a/docs/source/index.rst b/docs/source/index.rst index 0b07264..37cb0de 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,9 +1,28 @@ -.. QCEngine documentation master file, created by - sphinx-quickstart on Fri Aug 17 09:45:43 2018. +.. PES-Learn documentation master file, created by + sphinx-quickstart on Thu May 2 11:10:40 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -========= -PESLearn -========= +Welcome to PES-Learn's documentation! +===================================== +**PES-Learn** is a Python library designed to fit system-specific Born-Oppenheimer +potential energy surfaces using modern machine learning models. PES-Learn assists in +generating datasets, and features Gaussian process, neural network, and kernel ridge regression +model optimization routines. The goal is to provide high-performance models for a given dataset +*without* requiring user expertise in machine learning. + +This project is under active development and welcomes community suggestions and contributions. + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search`