# -*- coding: utf-8 -*-
#
# DO NOT EDIT conf.py! GO FOR conf.py.in, THERE IS VARIABLE SUBSTITUTION
# INVOLVED
#
# ProMod3 documentation build configuration file, originally created by
# sphinx-quickstart on Thu Oct 10 23:17:00 2013, then modified.
#
# 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.

# pylint: disable=invalid-name,missing-docstring

import sys
sys.dont_write_bytecode = True
# 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.
sys.path.insert(0, r'@LIB_STAGE_PATH@/@PYTHON_MODULE_PATH@')
sys.path.insert(1, r'@OST_PYMOD_PATH@')
sys.path.insert(2, r'@THIS_DIR@')
sys.path.insert(3, r'@PROJECT_SOURCE_DIR@/actions/tests/')

# -- 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.todo',
              'sphinx.ext.coverage',
              'sphinx.ext.mathjax',
              'sphinx.ext.ifconfig',
              'sphinx.ext.extlinks', 'cmake']

# Check first line of docstring for signatures (autofunction)
autodoc_docstring_signature = True

# 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.
master_doc = 'index'

# General information about the project.
project = u'ProMod3'
copyright = u'2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin

# 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 = '@PROMOD3_VERSION_MAJOR@.@PROMOD3_VERSION_MINOR@'
# The full version, including alpha/beta/rc tags.
release = '@PROMOD3_VERSION_MAJOR@.@PROMOD3_VERSION_MINOR@.@PROMOD3_VERSION_PATCH@'

# 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 %H:%M, %Y'

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

# 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 = 'sphinx'

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


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

# Since we use sphinx.ext.mathjax to render formulas on HTML pages: The
# MathJax web-page deprecated their own CDN to serve JavaScript but it is
# still the default for Sphinx. Here we redirect to the CDN recommended by
# MathJax.
mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML'


# 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 themes here, relative to this directory.
#html_theme_path = []

# 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

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

# The name of an image file (within the static path) to use as favicon of the
# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = 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".
html_static_path = list()

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

# 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 = ''

# 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 = 'ProMod3doc'


# -- 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': '',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
    ('index', 'ProMod3.tex', u'ProMod3 Documentation',
     u'Bienchen', '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

# 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 = [
    ('index', 'promod3', u'ProMod3 Documentation',
     [u'Bienchen'], 1)
]

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


# -- 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 = [
    ('index', 'ProMod3', u'ProMod3 Documentation',
     u'Bienchen', 'ProMod3', 'One line description of project.',
     'Miscellaneous'),
]

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

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

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None),
                       'openstructure': ('@OST_DOC_URL@', None)}

# -- ProMod3 specific configuration --------------------------------------------

extlinks = {'py_docs' : ('@PYTHON_DOC_URL@/%s',
                         'Python documentation'),
            'ost_docs' : ('@OST_DOC_URL@/%s',
                          'OpenStructure documentation')}

# The _nameattr is a bit ugly: we want to have __name__ formatted as Python
# attribute but Sphinx does not go with calling :attr: inside extlinks. To keep
# the Python url prefix, we define sth here. Same holds for _mainattr. But this
# time instead of printing '__name__' we want to see '__main__'.
rst_epilog = """
.. |project| replace:: %s
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
.. |ost_version| replace:: 2.3.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
.. |restructuredtext| replace:: reStructuredText
.. |restructuredtext_abrv| replace:: reST
.. |boost| replace:: Boost
.. |git| replace:: Git
.. |C++| replace:: C++
.. _ost_s: https://www.OpenStructure.org
.. _nameattr: @PYTHON_DOC_URL@/library/__main__.html
.. _mainattr: @PYTHON_DOC_URL@/library/__main__.html
.. _descattr: @PYTHON_DOC_URL@/library/argparse.html#description
.. _progattr: @PYTHON_DOC_URL@/library/argparse.html#prog
.. _argpinit: @PYTHON_DOC_URL@/library/argparse.html#argparse.ArgumentParser
.. _sysargv: @PYTHON_DOC_URL@/library/sys.html#sys.argv
.. |pep8| replace:: PEP 8
.. _pep8: https://www.python.org/dev/peps/pep-0008/
""" % project

# increase default timeout (5s) for linkcheck
linkcheck_timeout = 15

#  LocalWords:  cmake