# 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'
]

# 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']


# -- 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'

# 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 = {
    '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),
}

@@ -1584,16 +1584,56 @@
 ADME.md'
+,%0A    'narratives',%0A    'contributing',%0A
 %5D%0A%0A%0A# --

exclude unused docs from build