# -*- 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 = 'SINA'
copyright = '2019, Elmar Pruesse'
author = 'Elmar Pruesse'

# The full version, including alpha/beta/rc tags
release = '1.7.2'

# The short X.Y version
version = '.'.join(release.split('.')[:2])


# -- General configuration ---------------------------------------------------

# needs_sphinx = '1.0'

extensions = [
    'sphinx.ext.extlinks',
    'sphinx.ext.todo',
    'sphinx.ext.mathjax',
]

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
language = None
exclude_patterns = []
pygments_style = None


# -- Options for HTML output -------------------------------------------------

html_theme = 'alabaster'

# html_theme_options = {}

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 = 'SINAdoc'


# -- 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, 'SINA.tex', 'SINA Documentation',
     'Elmar Pruesse', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('commandline', 'sina', 'reference based multiple sequence alignment', [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, 'SINA', 'SINA Documentation',
     author, 'SINA', 'reference based multiple sequence alignment',
     'Bioinformatics'),
]


# -- 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 todo extension ----------------------------------------------

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

extlinks = {
    'biotools': ('https://bio.tools/%s', ''),
    'doi': ('https://doi.org/%s', ''),
    'issue': ('https://github.com/epruesse/SINA/issues/%s', '#')
}