# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- 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 = 'mOTUs'
copyright = '2024 | All rights reserved by the Sunagawa Lab'
author = 'Sunagawa Lab'

# The full version, including alpha/beta/rc tags
release = '4.0'


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

# 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_bootstrap_theme',
              'sphinx_design',
              "myst_parser"
]

myst_enable_extensions = ["colon_fence"]

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

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['Data_old.md', 'Quickstart.md', 'Tool.md', 'documentation/FAQ.md', 'documentation/GTDB_taxonomy.md', 'documentation/SNV_profiling.md', 'documentation/explore_motus_profile.md', 'documentation/install.md', 'documentation/long_reads.md', 'documentation/conceptual_implementation.md', 'documentation/options_manual.md', 'documentation/tutorial.md', 'documentation/tutorial_2.md']


# -- 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 = 'bootstrap'
html_logo = "images/motu_logo_small.png"
html_favicon = "images/motu_logo_small.png"
# 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']


html_theme_options = {
    # Navigation bar title. (Default: ``project`` value)
    'navbar_title': "mOTUs",

    # Tab name for entire site. (Default: "Site")
    'navbar_site_name': "Website",

    # A list of tuples containing pages or urls to link to.
    # Valid tuples should be in the following forms:
    #    (name, page)                 # a link to a page
    #    (name, "/aa/bb", 1)          # a link to an arbitrary relative url
    #    (name, "http://example.com", True) # arbitrary absolute url
    # Note the "1" or "True" value above as the third argument to indicate
    # an arbitrary url.
    'navbar_links': [
        ("Database", "Data"),
        ("Tool (Alpha)", "https://sunagawalab.ethz.ch/share/MOTUS/motus-tool/v4.0.0a/motus4.html", True),
        ("About", "About")
        # ("Quickstart", "Quickstart"),
    ],

    # Render the next and previous page links in navbar. (Default: true)
    'navbar_sidebarrel': False,

    # Render the current pages TOC in the navbar. (Default: true)
    'navbar_pagenav': False,

    # Tab name for the current pages TOC. (Default: "Page")
    'navbar_pagenav_name': "Page",

    # Global TOC depth for "site" navbar tab. (Default: 1)
    # Switching to -1 shows all levels.
    'globaltoc_depth': -1,

    # Include hidden TOCs in Site navbar?
    #
    # Note: If this is "false", you cannot have mixed ``:hidden:`` and
    # non-hidden ``toctree`` directives in the same page, or else the build
    # will break.
    #
    # Values: "true" (default) or "false"
    'globaltoc_includehidden': "false",

    # HTML navbar class (Default: "navbar") to attach to <div> element.
    # For black navbar, do "navbar navbar-inverse"
    'navbar_class': "navbar",

    # Fix navigation bar to top of page?
    # Values: "true" (default) or "false"
    'navbar_fixed_top': "true",

    # Location of link to source.
    # Options are "nav" (default), "footer" or anything else to exclude.
    'source_link_position': "exclude",

    # Bootswatch (http://bootswatch.com/) theme.
    #
    # Options are nothing (default) or the name of a valid theme
    # such as "cosmo" or "sandstone".
    #
    # The set of valid themes depend on the version of Bootstrap
    # that's used (the next config option).
    #
    # Currently, the supported themes are:
    # - Bootstrap 2: https://bootswatch.com/2
    # - Bootstrap 3: https://bootswatch.com/3
    'bootswatch_theme': "sandstone",

    # Choose Bootstrap version.
    # Values: "3" (default) or "2" (in quotes)
    'bootstrap_version': "3",
}


html_sidebars = {
      "**": ["localtoc.html"]
   }