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# 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:
# http://www.sphinx-doc.org/en/master/config
# -- 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 -----------------------------------------------------
from augur.__version__ import __version__ as augur_version
from datetime import date
import subprocess
def git_authors():
result = subprocess.run(
["git", "shortlog", "--summary", "HEAD"],
stdout = subprocess.PIPE,
check = True)
names = [
line.strip().split("\t")[1]
for line in result.stdout.decode("utf-8").splitlines()
]
return names
def prose_list(items):
if not items:
return ""
if len(items) == 1:
return items[0]
elif len(items) == 2:
return " and ".join(items)
else:
return ", ".join([*items[0:-1], "and " + items[-1]])
project = 'Augur'
version = augur_version
release = version
copyright = '2014–%d Trevor Bedford and Richard Neher' % (date.today().year)
author = prose_list(git_authors())
# -- 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.autodoc',
'sphinxarg.ext',
'sphinx.ext.napoleon',
'sphinx_autodoc_typehints', # must come after napoleon https://github.com/tox-dev/sphinx-autodoc-typehints/blob/1.21.4/README.md#compatibility-with-sphinxextnapoleon
'sphinx_markdown_tables',
'sphinx.ext.intersphinx',
'sphinx_tabs.tabs',
'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',
'contribute/DEV_DOCS.md',
'faq/colors.md',
'faq/fasta_input.md',
'faq/import-beast.md',
'faq/lat_longs.md',
'faq/seq_traits.md',
'faq/translate_ref.md',
'faq/vcf_input.md',
'usage/augur_snakemake.md',
]
# A string of reStructuredText that will be included at the end of every source
# file that is read. This is a possible place to add substitutions that should
# be available in every file.
rst_epilog = f"""
.. |authors| replace:: {author}
"""
# -- 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
}
# 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']
# These paths are either relative to html_static_path
# or fully qualified paths (eg. https://...)
html_css_files = [
'css/custom.css',
]
# -- Resolve build warnings --------------------------------------------------
nitpick_ignore = [
# These are valid numpydoc keywords¹, but somehow they are not recognized by
# napoleon.
# ¹ https://numpydoc.readthedocs.io/en/v1.5.0/format.html#parameters
('py:class', 'optional'),
('py:class', 'iterable'),
# Some references get translated to these, but somehow they can't get
# resolved by intersphinx for a proper link.
("py:class", "json.decoder.JSONDecodeError"),
("py:class", "json.encoder.JSONEncoder"),
]
# -- Cross-project references ------------------------------------------------
intersphinx_mapping = {
'Bio': ('https://biopython.org/docs/latest/api/', None),
'docs.nextstrain.org': ('https://docs.nextstrain.org/en/latest/', None),
'cli': ('https://docs.nextstrain.org/projects/cli/en/stable', None),
'python': ('https://docs.python.org/3', None),
'numpy': ('https://numpy.org/doc/stable', None),
'pandas': ('https://pandas.pydata.org/docs', None),
'treetime': ('https://treetime.readthedocs.io/en/stable/', None),
}
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