#!/usr/bin/env python3

# -*- coding: utf-8 -*-

#

# SingleCellMultiOmics documentation build configuration file, created by

# sphinx-quickstart on Tue Jul 16 11:59:02 2019.

#

# This file is execfile()d with the current directory set to its

# containing dir.

#

# Note that not all possible configuration values are present in this

# autogenerated file.

#

# All configuration values have a default; values that are commented out

# serve to show the default.

# 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

import glob

#sys.path.insert(0, os.path.abspath('../singlecellmultiomics/'))

sys.path.insert(0, os.path.abspath('../singlecellmultiomics'))

import sphinx_rtd_theme

# -- 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.autosummary',

    'sphinx.ext.autodoc',

    'sphinx.ext.coverage',

    #'sphinx.ext.mathjax',

    'sphinx.ext.viewcode',

    'sphinx.ext.githubpages','sphinx.ext.napoleon']

# Napoleon settings

napoleon_google_docstring = True

napoleon_numpy_docstring = True

napoleon_include_init_with_doc = False

napoleon_include_private_with_doc = False

napoleon_include_special_with_doc = True

napoleon_use_admonition_for_examples = False

napoleon_use_admonition_for_notes = False

napoleon_use_admonition_for_references = False

napoleon_use_ivar = False

napoleon_use_param = True

napoleon_use_rtype = True

add_module_names = True

# 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.

project = 'SingleCellMultiOmics'

copyright = '2019, Buys de Barbanson, Jake Yeung'

author = 'Buys de Barbanson, Jake Yeung'

# 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.

version = '0.0.2'

# The full version, including alpha/beta/rc tags.

release = '0.0.2'

# 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 patterns also effect to html_static_path and html_extra_path

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.

pygments_style = 'sphinx'

# If true, `todo` and `todoList` produce output, else they produce nothing.

todo_include_todos = False

# -- 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_static_path = ['_static']

# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.

htmlhelp_basename = 'SingleCellMultiOmicsdoc'

# -- 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, 'SingleCellMultiOmics.tex', 'SingleCellMultiOmics Documentation',

     'Buys de Barbanson, Jake Yeung', '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, 'singlecellmultiomics', 'SingleCellMultiOmics 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, 'SingleCellMultiOmics', 'SingleCellMultiOmics Documentation',

     author, 'SingleCellMultiOmics', 'One line description of project.',

     'Miscellaneous'),

]