Add doc example

docs/UsersGuide/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+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)

docs/UsersGuide/README

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+Steps to build and use the Sphinx documentation tool:
+
+1) Get Sphinx, sphinxcontrib-bibtex, and the RTD theme installed on your desktop from
+    http://www.sphinx-doc.org/en/master/usage/installation.html
+    https://sphinxcontrib-bibtex.readthedocs.io/en/latest/quickstart.html#installation
+    https://pypi.org/project/sphinx-rtd-theme/
+
+    For example: 
+    pip install sphinx
+    pip install sphinxcontrib-bibtex
+    pip install sphinx-rtd-theme
+
+    One approach that has worked to resolve "Module Not Found" errors for users with MacPorts package manager: 
+    $ sudo port install py-six  # may not be necessary
+    $ sudo port install py310-sphinxcontrib-bibtex
+    $ sudo port select --set sphinx py310-sphinx
+    $ sudo port install py310-sphinx_rtd_theme
+
+    py310 can be replaced with the user's version of Python (e.g., py39) 
+
+To build html:
+
+$ cd MOM6_OBGC_examples/docs/UsersGuide
+$ make clean && sphinx-build -b html source build
+
+The "make html" command can often be used in place of the previous command.
+
+Sphinx uses Latex to export the documentation as a PDF file.  To build pdf:
+
+make latexpdf
+
+It will generate a PDF file in ./build/latex/<sphinx-project-name>.pdf

docs/UsersGuide/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/UsersGuide/requirements.txt

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+sphinxcontrib-bibtex
+sphinx_rtd_theme
+docutils==0.16

docs/UsersGuide/source/Introduction.rst

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+.. _Intro:
+
+****************
+Introduction
+****************
+
+This User's Guide provides guidance for setting and running the MOM6 Ocean Biogeochemical System.
+
+The Ocean Biogeochemical component is based on :cite:t:`StockEtAl2019` (2019)
+
+Disclaimer 
+*************
+
+The United States Department of Commerce (DOC) GitHub project code is
+provided on an “as is” basis and the user assumes responsibility for its
+use. DOC has relinquished control of the information and no longer has a
+responsibility to protect the integrity, confidentiality, or
+availability of the information. Any claims against the Department of
+Commerce stemming from the use of its GitHub project will be governed by
+all applicable Federal laws. Any reference to specific commercial
+products, processes, or services by service mark, trademark,
+manufacturer, or otherwise, does not constitute or imply their
+endorsement, recommendation, or favoring by the Department of Commerce.
+The Department of Commerce seal and logo, or the seal and logo of a DOC
+bureau, shall not be used in any manner to imply endorsement of any
+commercial product or activity by DOC or the United States Government.
+
+References
+*************
+
+.. bibliography:: references.bib

docs/UsersGuide/source/_static/custom.css

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+.red { color: red; }
+.bolditalic {
+  font-family: "Courier New", Courier, monospace;
+  font-weight: bold;
+  font-style: italic;
+}
+
+.underline {
+   text-decoration: underline;
+}
+
+.bolditalic {
+   font-weight: bold;
+   font-style: italic;
+}
+
+table.align-default {
+   margin-left: 0px;
+   margin-right: auto;
+}
+
+table.align-center {
+   margin-left: 0px;
+   margin-right: auto;
+}

docs/UsersGuide/source/_static/theme_overrides.css

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+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-nav-content {
+      max-width: 100% !important;
+   }
+
+   /* .wy-table-responsive { */
+   /*   overflow: visible !important; */
+   /* } */
+
+}
+
+
+

docs/UsersGuide/source/_templates/.gitignore

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+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

docs/UsersGuide/source/conf.py

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+# -*- 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
+
+# -- 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('.'))
+
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'MOM6_OBGC_examples Users Guide'
+copyright = '2023, '
+author = ' '
+
+# The short X.Y version
+version = 'develop'
+# The full version, including alpha/beta/rc tags
+release = 'Develop Branch Documentation'
+
+numfig = True
+
+# -- 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_rtd_theme',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+    'sphinxcontrib.bibtex',
+]
+
+bibtex_bibfiles = ['references.bib']
+#bibtex_bibfiles = ['refs.bib']
+
+# 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 = None
+
+# 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 = 'sphinx'
+
+
+# -- 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'
+html_theme_path = ["_themes", ]
+
+# 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 = {}
+html_theme_options = {"body_max_width": "none"}
+
+# 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_static_path = []
+html_static_path = ['_static']
+html_context = {}
+
+def setup(app):
+    app.add_css_file('custom.css')  # may also be an URL
+    app.add_css_file('theme_overrides.css')  # may also be a URL
+
+# 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 = 'MOM6_OBGC_examples'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_engine = 'pdflatex'
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+      'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+      'pointsize': '11pt',
+
+    # Additional stuff for the LaTeX preamble.
+      'preamble': r'''
+        \usepackage{charter}
+        \usepackage[defaultsans]{lato}
+        \usepackage{inconsolata}
+    ''',
+    # Release name prefix
+      'releasename': ' ',
+
+    # 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, 'MOM6_OBGC_examples.tex', 'MOM6_OBGC_examples Users Guide',
+     ' ', '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, 'MOM6_OBGC_examples', 'MOM6_OBGC_examples Users Guide',
+     [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, 'MOM6_OBGC_examples', 'MOM6_OBGC_examples Users Guide',
+     author, 'MOM6_OBGC_examples', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+   'MOM6_OBGC_examples': ('https://MOM6_OBGC_examples.readthedocs.io/en/latest/', None),
+}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True