# 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 = 'Auspice'
copyright = '2020, James Hadfield, Trevor Bedford and Richard Neher'
author = 'James Hadfield, Trevor Bedford and Richard Neher'


# -- 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 = [
    'recommonmark',
    'sphinx.ext.intersphinx',
    'sphinx_markdown_tables',
    'sphinxarg.ext',
    'sphinx.ext.autodoc',
    'nextstrain.sphinx.theme',
]

# 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 = ['_build', 'Thumbs.db', '.DS_Store', 'README.md',
    'narratives',
]


# -- 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 = 'nextstrain-sphinx-theme'

html_theme_options = {
    'logo_only': False, # if True, don't display project name at top of the sidebar
    'collapse_navigation': False, # if True, no [+] icons in sidebar
    'titles_only': True, # if True, page subheadings not included in nav
}


# -- Cross-project references ------------------------------------------------

intersphinx_mapping = {
    'docs.nextstrain.org': ('https://docs.nextstrain.org/en/latest/', None),
}

# -- Math rendering <https://github.com/hagenw/sphinxcontrib-katex>  ---------

extensions.append('sphinxcontrib.katex')

# Pre-render math (avoids the browser loading the JS library, at the expense
# of a more complex build
katex_prerender = True

# We could change the default CDN link & store within our /assets if wanted
katex_css_path = 'https://cdn.jsdelivr.net/npm/katex@0.16.10/dist/katex.min.css'

# -- Linkchecking ------------------------------------------------------------

## NOTE: for both sets of regular expressions that follow, the
## underlying linkchecker code uses `re.match()` to apply them to URLs
## — so there's already an implicit "only at the beginning of a
## string" matching happening, and something like a plain `r'google'`
## regular expression will _NOT_ match all google.com URLs.
linkcheck_ignore = [
     # we have links to localhost for explanatory purposes; obviously
     # they will never work in the linkchecker
     r'^http://localhost:\d+',
     # These URLs are valid but return broken when using linkcheck. They can still be checked manually.
     r'^https://academic\.oup\.com/bioinformatics/article/34/23/4121/5001388',
     r'https://www\.gnu\.org/licenses/agpl-3\.0\.en\.html',
     r'https://www\.npmjs\.com/package/auspice',
]
linkcheck_anchors_ignore_for_url = [
     # Github uses anchor-looking links for highlighting lines but
     # handles the actual resolution with Javascript, so skip anchor
     # checks for Github URLs:
     r'^https://github\.com',
]