#!/usr/bin/env python

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

#

# openomics documentation build configuration file, created by

# sphinx-quickstart on Fri Jun  9 13:47:02 2017.

#

# 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

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

import openomics

# 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.autosummary',

    'sphinx_autodoc_typehints',

    'sphinx.ext.linkcode',

    'sphinx.ext.napoleon',

    'myst_parser',

    # User Usability

    'sphinx_copybutton',

    'sphinx_inline_tabs',

    'sphinx.ext.coverage',

    'sphinx.ext.intersphinx',

    "sphinx.ext.viewcode",

    'sphinx_automodapi.automodapi',

    'sphinx_automodapi.smart_resolver',

    'sphinx.ext.graphviz',

    'sphinx.ext.inheritance_diagram',

]

autosummary_generate = False

autosummary_imported_members = True

napoleon_google_docstring = True

napoleon_use_param = True

napoleon_use_ivar = True

# Add any paths that contain templates here, relative to this directory.

templates_path = ['_templates']

exclude_patterns = ['_build', '_templates']

# The suffix(es) of source filenames.

# You can specify multiple suffix as a list of string:

#

source_suffix = {

    '.rst': 'restructuredtext',

    '.txt': 'markdown',

    '.md': 'markdown',

}

# The master toctree document.

master_doc = 'index'

# General information about the project.

project = 'OpenOmics'

copyright = "2019, Nhat Tran"

author = "Jonny Tran"

# 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 = openomics.__version__

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

release = openomics.__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 = 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 = True

# -- Options for Markdown files ----------------------------------------------

myst_enable_extensions = ["colon_fence", "deflist"]

myst_heading_anchors = 3

# -- 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 = 'furo'

# 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 = {

    "sidebar_hide_name": False,

    "light_css_variables": {

        # "color-brand-primary": "#ff5c84",

        # "color-brand-content": "#ff5c84",

        # "color-admonition-background": "#33cccc",

        # "font-stack": "Arial, sans-serif",

        # "font-stack--monospace": "Courier, monospace",

    },

}

html_logo = "../openomics_web/assets/openomics_logo.png"

html_favicon = '_static/favicon.png'

pygments_style = "sphinx"

pygments_dark_style = "monokai"

# 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']

graphviz_dot = "/usr/bin/dot"

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

# Output file base name for HTML help builder.

htmlhelp_basename = 'openomicsdoc'

# -- 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, 'openomics',

     u'OpenOmics Documentation',

     [author], 1)

]

def linkcode_resolve(domain, info):

    if domain != 'py':

        return None

    if not info['module']:

        return None

    filename = info['module'].replace('.', '/')

    return "https://github.com/JonnyTran/OpenOmics/%s.py" % filename