# -*- coding: utf-8 -*-
#
# dms_variants documentation build configuration file.
#
# 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.
"""Configuration file for sphinx."""

import datetime
import os
import re
import sys

sys.path.insert(0, '{0}/..'.format(os.path.abspath('.')))


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

# If your documentation needs a minimal Sphinx version, state it here.
#
needs_sphinx = '1.0'

numfig = False

# 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.doctest',
        'sphinx.ext.mathjax',
        'sphinx.ext.githubpages',
        'sphinx.ext.viewcode',
        'sphinx.ext.napoleon',
        'matplotlib.sphinxext.plot_directive',
        'nbsphinx',
        'nbsphinx_link',
        ]

# configuration to matplotlib.sphinxext.plot_directive
plot_include_source = True
plot_html_show_source_link = False
# https://github.com/matplotlib/matplotlib/issues/4563#issuecomment-381366101
plot_rcparams = {'savefig.bbox': 'tight'}
plot_apply_rcparams = 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 = u'dms_variants'
copyright = f"2019--{datetime.datetime.now().year}"  # noqa: A001
author = u'`the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_'

# 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.
# Read in the version from file
versionfile = os.path.abspath(os.path.join(
        os.path.dirname(__file__), '../dms_variants/__init__.py'))
with open(versionfile) as f:
    versiontext = f.read()
versionmatches = re.findall(
            r'__version__\s+=\s+[\'"]([^\'"]+)[\'"]',
            versiontext)
if len(versionmatches) != 1:
    raise ValueError(f"found {len(versionmatches)} matches for version "
                     f"in {versionfile}")
else:
    versionstring = versionmatches[0]
# The full version, including alpha/beta/rc tags.
release = versionstring

# 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', 'README.rst',
                    'doc_requirements.txt', '**.ipynb_checkpoints']

# 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 = 'alabaster'

# 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 = {
        'logo': 'BloomLogo.jpg',
        'logo_name': 'true',
        'description': 'Analyze deep mutational scanning of barcoded variants',
        'github_button': 'true',
        'github_user': 'jbloomlab',
        'github_repo': 'dms_variants',
        'github_banner': 'true',
        'travis_button': 'true',
        'sidebar_width': '250px',
        }

# 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 = 'dms_variantsdoc'


# -- 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, 'dms_variants.tex', u'dms_variants Documentation',
     u'`the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_', '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, 'dms_variants', u'dms_variants 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, 'dms_variants', u'dms_variants Documentation',
     author, 'dms_variants',
     'Analyze deep mutational scanning of barcoded variants',
     'Miscellaneous'),
    ]
