#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Biopython Sphinx documentation build configuration file.

After generating ``*.rst`` files from the source code, this
file controls running ``sphinx-build`` to turn these into
human readable documentation.
"""

import os
import shutil
# import sys
import tempfile

from Bio import __version__

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

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
needs_sphinx = '1.8'

# 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.todo',
              'sphinx.ext.viewcode',
              'sphinx.ext.autosummary',
              'numpydoc']

# 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 = 'Biopython'
copyright = '1999-2017, The Biopython Contributors'
author = 'The Biopython Contributors'
document = 'Biopython API Documentation'

# 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 = __version__  # TODO: Shorten this
# The full version, including alpha/beta/rc tags.
release = __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 = 'en'

# 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 autodoc --------------------------------------------------

# This requires Sphinx 1.8.0b1 or later:
autodoc_default_values = {
    'members': None,
    'undoc-members': None,
    'special-members': None,
    'show-inheritance': None,
    'member-order': 'bysource',
    'exclude-members': '__dict__,__weakref__,__module__',
}

# To avoid import errors.
autodoc_mock_imports = ['MySQLdb']

# -- 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 = {}

# 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 = 'Biopython_doc'


# -- 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, 'Biopython_API.tex', document, author, '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, 'biopython', document, [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, 'Biopython', document, author, 'Biopython',
     'Collection of modules for dealing with biological data in Python.',
     'Miscellaneous'),
]


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

# Bibliographic Dublin Core info.
epub_title = document  # project
epub_author = author
epub_publisher = author
epub_copyright = copyright

# 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']

# -- Options for numpydoc -------------------------------------------------

numpydoc_class_members_toctree = False

# -- Magic to run sphinx-apidoc automatically -----------------------------

# See https://github.com/rtfd/readthedocs.org/issues/1139
# on which this is based.


def run_apidoc(_):
    """Call sphinx-apidoc on Bio and BioSQL modules."""
    from sphinx.ext.apidoc import main as apidoc_main
    cur_dir = os.path.abspath(os.path.dirname(__file__))
    # Can't see a better way than running apidoc twice, for Bio & BioSQL
    # We don't care about the index.rst / conf.py (we have our own)
    # or the Makefile / make.bat (effectively same) clashing,
    # $ sphinx-apidoc -e -F -o /tmp/api/BioSQL BioSQL
    # $ sphinx-apidoc -e -F -o /tmp/api/Bio Bio
    tmp_path = tempfile.mkdtemp()
    apidoc_main(['-e', '-F', '-o', tmp_path, '../../BioSQL'])
    apidoc_main(['-e', '-F', '-o', tmp_path, '../../Bio'])
    os.remove(os.path.join(tmp_path, 'index.rst'))  # Using our own
    for filename in os.listdir(tmp_path):
        if filename.endswith(".rst"):
            shutil.move(os.path.join(tmp_path, filename),
                        os.path.join(cur_dir, filename))
    shutil.rmtree(tmp_path)


def setup(app):
    """Over-ride Sphinx setup to trigger sphinx-apidoc."""
    app.connect('builder-inited', run_apidoc)