# -*- coding: utf-8 -*-
#
# MDAnalysis documentation build configuration file, created by
# sphinx-quickstart on Mon Sep 27 09:39:55 2010.
#
# 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.

import sys
import os
import datetime
import MDAnalysis as mda

# Custom MDA Formating
from pybtex.style.formatting.unsrt import Style as UnsrtStyle
from pybtex.style.labels import BaseLabelStyle
from pybtex.plugin import register_plugin

# 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.

# make sure sphinx always uses the current branch
sys.path.insert(0, os.path.abspath("../../.."))

# -- 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.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.mathjax",
    "sphinx.ext.viewcode",
    "sphinx.ext.napoleon",
    "sphinx.ext.todo",
    "sphinx_sitemap",
    "mdanalysis_sphinx_theme",
    "sphinxcontrib.bibtex",
    "sphinx.ext.doctest",
]

bibtex_bibfiles = ["references.bib"]


# Define custom MDA style for references
class KeyLabelStyle(BaseLabelStyle):
    def format_labels(self, entries):
        entry_list = []
        for entry in entries:
            author = str(entry.persons["author"][0]).split(",")[0]
            year = entry.fields["year"]
            entry_list.append(f"{author}{year}")
        return entry_list


class KeyStyle(UnsrtStyle):
    default_label_style = "keylabel"


register_plugin("pybtex.style.labels", "keylabel", KeyLabelStyle)
register_plugin("pybtex.style.formatting", "MDA", KeyStyle)

mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"

# for sitemap with https://github.com/jdillard/sphinx-sitemap
# This sitemap is correct both for the development and release docs, which
# are both served from docs.mdanalysis.org/$version .
# The docs used to be available automatically at mdanalysis.org/mdanalysis;
# they are now at docs.mdanalysis.org/, which requires a CNAME DNS record
# pointing to mdanalysis.github.io. To change this URL you should change/delete
# the CNAME record for "docs" and update the URL in GitHub settings
site_url = "https://docs.mdanalysis.org/"

# Add any paths that contain templates here, relative to this directory.
# templates_path = ['_templates']

# The suffix of source filenames.
source_suffix = ".rst"

# The encoding of source files.
# source_encoding = 'utf-8-sig'

# The master toctree document.
# 'index' has the advantage that it is immediately picked up by the webserver
master_doc = "index"

# General information about the project.
# (take the list from AUTHORS)
# Ordering: (1) Naveen (2) Elizabeth, then all contributors in alphabetical order
#           (last) Oliver
author_list = mda.__authors__
authors = ", ".join(author_list[:-1]) + ", and " + author_list[-1]
project = "MDAnalysis"
now = datetime.datetime.now()
copyright = "2005-{}, ".format(now.year) + authors

# 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.
#
# Dynamically calculate the version
packageversion = __import__("MDAnalysis").__version__
# The short X.Y version.
# version = '.'.join(packageversion.split('.')[:2])
version = packageversion  # needed for right sitemap.xml URLs
# The full version, including alpha/beta/rc tags.
release = packageversion

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
# today = ''
# Else, today_fmt is used as the format for a strftime call.
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ["_build"]

# The reST default role (used for this markup: `text`) to use for all documents.
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = "default"

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# to include decorated objects like __init__
autoclass_content = "both"

# to prevent including of member entries in toctree
toc_object_entries = 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 = "mdanalysis_sphinx_theme"

extra_nav_links = {}
extra_nav_links["MDAnalysis"] = "http://mdanalysis.org"
extra_nav_links["User guide"] = "http://userguide.mdanalysis.org"
extra_nav_links["MDAKits"] = "https://mdakits.mdanalysis.org/"


html_theme_options = {
    "mda_official": True,
    "extra_nav_links": extra_nav_links,
}

# 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_context = {
    "versions_json_url": "https://docs.mdanalysis.org/versions.json"
}

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
# html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.
# html_short_title = None

# 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".
# For RTD theme: custom.css to override theme defaults.
html_static_path = []

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
# html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
# alabaster sidebars
html_sidebars = {
    "**": [
        "about.html",
        "navigation.html",
        "relations.html",
        "searchbox.html",
    ]
}

# Additional templates that should be rendered to pages, maps page names to
# template names.
# html_additional_pages = {}

# If false, no module index is generated.
# html_domain_indices = True

# If false, no index is generated.
# html_use_index = True

# If true, the index is split into individual pages for each letter.
# html_split_index = False

# If true, links to the reST sources are added to the pages.
# html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
# html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
html_use_opensearch = "https://docs.mdanalysis.org"

# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = "MDAnalysisdoc"


# -- Options for LaTeX output --------------------------------------------------

# The paper size ('letter' or 'a4').
# latex_paper_size = 'letter'

# The font size ('10pt', '11pt' or '12pt').
# latex_font_size = '10pt'

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
    ("MDAnalysis.tex", "MDAnalysis Documentation", authors, "manual"),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
# latex_use_parts = False

# If true, show page references after internal links.
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
# latex_show_urls = False

# Additional stuff for the LaTeX preamble.
# latex_preamble = ''

# Documents to append as an appendix to all manuals.
# latex_appendices = []

# If false, no module index is generated.
# latex_domain_indices = True


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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [("mdanalysis", "MDAnalysis Documentation", [authors], 1)]


# -- Options for Epub output ---------------------------------------------------

# Bibliographic Dublin Core info.
epub_title = "MDAnalysis"
epub_author = authors
epub_publisher = "Arizona State University, Tempe, Arizona, USA"
epub_copyright = "2015, " + authors

# The language of the text. It defaults to the language option
# or en if the language is not set.
# epub_language = ''

# The scheme of the identifier. Typical schemes are ISBN or URL.
# epub_scheme = ''

# 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 = ''

# HTML files that should be inserted before the pages created by sphinx.
# The format is a list of tuples containing the path and title.
# epub_pre_files = []

# HTML files shat should be inserted after the pages created by sphinx.
# The format is a list of tuples containing the path and title.
# epub_post_files = []

# A list of files that should not be packed into the epub file.
# epub_exclude_files = []

# The depth of the table of contents in toc.ncx.
# epub_tocdepth = 3

# Allow duplicate toc entries.
# epub_tocdup = True


# Configuration for intersphinx: refer to the Python standard library
# and other packages used by MDAnalysis
intersphinx_mapping = {
    "h5py": ("https://docs.h5py.org/en/stable", None),
    "python": ("https://docs.python.org/3/", None),
    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
    "gsd": ("https://gsd.readthedocs.io/en/stable/", None),
    "maplotlib": ("https://matplotlib.org/stable/", None),
    "griddataformats": ("https://mdanalysis.org/GridDataFormats/", None),
    "pmda": ("https://mdanalysis.org/pmda/", None),
    "networkx": ("https://networkx.org/documentation/stable/", None),
    "numpy": ("https://numpy.org/doc/stable/", None),
    "parmed": ("https://parmed.github.io/ParmEd/html/", None),
    "rdkit": ("https://rdkit.org/docs/", None),
    "waterdynamics": ("https://www.mdanalysis.org/waterdynamics/", None),
    "pathsimanalysis": ("https://www.mdanalysis.org/PathSimAnalysis/", None),
    "mdahole2": ("https://www.mdanalysis.org/mdahole2/", None),
    "dask": ("https://docs.dask.org/en/stable/", None),
}
