Replaced auto-generated conf.py with original.

docs/conf.py

@@ -1,26 +1,192 @@
-# Configuration file for the Sphinx documentation builder.
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
 #
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# vplanet documentation build configuration file, created by
+# sphinx-quickstart on Wed Aug  9 19:49:05 2017.
+#
+
+import sys
+import os
+sys.path.insert(0, os.path.abspath('sphinx_rtd_theme'))
+import glob
+import sphinx_rtd_theme
+import datetime
+
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../examples'))
+srcdir = os.path.join(os.path.dirname(
+    os.path.dirname(os.path.abspath(__file__))), 'src')
+srcfiles = [os.path.basename(x)
+            for x in glob.glob(os.path.join(srcdir, '*.[ch]'))]
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
 
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.todo',
+              'sphinx.ext.coverage',
+              'sphinx.ext.mathjax',
+              'breathe',
+              'sphinx_rtd_theme',
+              'matplotlib.sphinxext.plot_directive']
+
+plot_include_source = False
+plot_html_show_source_link = False
+plot_html_show_formats = False
+
+# Breathe bridge to Doxygen C docs
+breathe_default_project = "VPLanet"
+breathe_projects_source = {"VPLanet": (srcdir, srcfiles)}
+
+# 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'
+
+# General information about the project.
+today = datetime.date.today()
+year = today.year
 
 project = 'VPLanet'
-copyright = '2024, Rory Barnes et al.'
+copyright = '2018-'+repr(year)+', The VPLanet Team'
 author = 'Rory Barnes et al.'
-release = '0.0.1'
 
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+# Prologue to be included in all .rst files
+# Handy for defining shortcuts / roles!
+rst_prolog = """
+"""
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+with open(os.path.join('..', 'VERSION')) as f:
+    version = f.read()
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# 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 = English
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['.build', 'Thumbs.db', '.DS_Store']
 
-extensions = []
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
 
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
 
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+if not on_rtd:  # only import and set the theme if we're building docs locally
+    html_theme = 'sphinx_rtd_theme'
+    html_theme_path = ['.themes', ]
+    html_theme_options = {"display_version": True}
 
 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_static_path = ['.static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html'
+    ],
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'vplanetdocs'
+
+
+# -- 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, 'vplanet.tex', 'VPLanet Documentation',
+     'Rory Barnes', '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, 'vplanet', 'VPLanet 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, 'vplanet', 'VPLanet Documentation',
+     author, 'vplanet', 'The Virtual Planet Simulator',
+     'Miscellaneous'),
+]