conf.py

# -*- coding: utf-8 -*-
#
# Hail documentation build configuration file, created by
# sphinx-quickstart on Fri Nov  4 10:55:10 2016.
#
# 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.

# 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 re
import sys
import datetime

sys.path.insert(0, os.path.abspath('./_ext'))

# sys.path.insert(0, os.path.abspath('.'))
# import sphinx_rtd_theme

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

nitpicky = True

# If your documentation needs a minimal Sphinx version, state it here.
#
needs_sphinx = '1.5.4'

# 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.doctest',
    'sphinxcontrib.katex',
    'sphinx.ext.viewcode',
    'sphinx.ext.autosummary',
    'nbsphinx',
    # https://github.com/spatialaudio/nbsphinx/issues/24#issuecomment-187172022 and https://github.com/ContinuumIO/anaconda-issues/issues/1430
    'IPython.sphinxext.ipython_console_highlighting',
    'sphinx.ext.napoleon',
    'sphinx.ext.intersphinx'
]

katex_css_path = \
    'https://cdn.jsdelivr.net/npm/katex@0.12.0/dist/katex.min.css'
katex_js_path = \
    'https://cdn.jsdelivr.net/npm/katex@0.12.0/dist/katex.min.js'
katex_autorender_path = \
    'https://cdn.jsdelivr.net/npm/katex@0.12.0/dist/contrib/auto-render.min.js'
katex_inline = [r'\(', r'\)']
katex_display = [r'\[', r'\]']
katex_prerender = False
katex_options = ''

nbsphinx_timeout = 300
nbsphinx_allow_errors = False
# F821 undefined name 'tags'
if not tags.has('checktutorial'):  # noqa: F821
    nbsphinx_execute = 'never'

autosummary_generate = ['api.rst',
                        'genetics/index.rst',
                        'methods/index.rst',
                        'methods/impex.rst',
                        'methods/stats.rst',
                        'methods/genetics.rst',
                        'methods/misc.rst',
                        'utils/index.rst',
                        'linalg/index.rst',
                        'stats/index.rst',
                        'expressions.rst',
                        'functions/index.rst',
                        'functions/core.rst',
                        'functions/constructors.rst',
                        'functions/string.rst',
                        'functions/stats.rst',
                        'functions/collections.rst',
                        'functions/numeric.rst',
                        'functions/genetics.rst',
                        ]
# autoclass_content = "both"
autodoc_default_flags = ['members', 'undoc-members']
autodoc_typehints = 'none'  # https://github.com/hail-is/hail/pull/9403#issuecomment-703776111

napoleon_use_rtype = False
napoleon_use_param = False

intersphinx_mapping = {
    'python': ('https://docs.python.org/3.7', None),
    'PySpark': ('https://spark.apache.org/docs/latest/api/python/', None),
    'Bokeh': ('https://docs.bokeh.org/en/1.2.0/', None),
    'numpy': ('https://numpy.org/doc/stable/', None),
    'scipy': ('https://docs.scipy.org/doc/scipy-1.3.3/reference', None),
    'pandas': ('https://pandas.pydata.org/docs/', None)}

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

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
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'Hail'
copyright = u'2015-{}, Hail Team'.format(datetime.datetime.now().year)
author = u'Hail Team'

# 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 full version, including alpha/beta/rc tags.
with open('../hail_version') as f:
    release = f.read().strip()
    version = re.match('[0-9]+.[0-9]+', release)[0]

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
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, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**/.ipynb_checkpoints']

# 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 = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False


# -- 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 = 'sphinx_rtd_theme'
# 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 = {
    'collapse_navigation': True,
    'display_version': True
}

# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = ["_themes", ]

# The name for this set of Sphinx documents.
# "<project> v<release> documentation" by default.
#
html_title = u'Hail'

# 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 (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
html_favicon = "misc/hail_logo_sq.ico"

# 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']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#
html_extra_path = ['misc/']

# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
html_last_updated_fmt = ''

# 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 = {
    '**': ['globaltoc.html', 'localtoc.html', 'searchbox.html']
}

# 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 = False

# 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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
#
# html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
# 'zh' user can custom change `jieba` dictionary path.
#
# html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#
# html_search_scorer = 'scorer.js'

# Output file base name for HTML help builder.
htmlhelp_basename = 'haildoc'

# -- 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': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'Hail.tex', u'Hail Documentation',
     u'Hail Team', '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 = []

# It false, will not define \strong, \code, 	itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True

# 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 = [
    (master_doc, 'hail', u'Hail Documentation',
     [author], 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 = [
    (master_doc, 'Hail', u'Hail Documentation',
     author, 'Hail', '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'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False


def autodoc_skip_member(app, what, name, obj, skip, options):
    exclusions = ('__delattr__', '__dict__', '__dir__', '__doc__', '__format__',
                  '__getattribute__', '__hash__', '__init__',
                  '__init_subclass__', '__new__', '__reduce__', '__reduce_ex__',
                  '__repr__', '__setattr__', '__sizeof__', '__str__',
                  '__subclasshook__', '__weakref__')
    exclude = name in exclusions
    return skip or exclude


def setup(app):
    app.connect('autodoc-skip-member', autodoc_skip_member)