stage docs

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
 

docs/requirements.yml

@@ -3,7 +3,7 @@ channels:
     - nodefaults
     - conda-forge
 dependencies:
-    - python=3
+    - python=3.8
     - sphinx
     - sphinx_rtd_theme
     - sphinx-automodapi

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

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`