conf.py

# Based on https://www.sphinx-doc.org/en/master/usage/configuration.html
#
# 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.

from docutils.statemachine import StringList
from docutils.parsers.rst import directives
from sphinx.ext.autosummary import Autosummary
import sphinx.ext.autosummary
from inspect import getmembers, isclass, isfunction
from importlib import import_module
from sphinx import addnodes
from docutils import nodes
import sphinx.domains.python
import sys
import os
import datetime
import connectomics
import pytorch_sphinx_theme


sys.path.insert(0, os.path.abspath("../.."))

# 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.

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

# If your documentation needs a minimal Sphinx version, state it here.
#
needs_sphinx = '3.0'

# 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.autosummary",
    "sphinx.ext.doctest",
    "sphinx.ext.intersphinx",
    "sphinx.ext.todo",
    "sphinx.ext.coverage",
    "sphinx.ext.napoleon",
    "sphinx.ext.viewcode",
    "sphinx.ext.autosectionlabel",
]

# katex option
katex_prerender = True

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

# 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.
author = 'PyTorch Connectomics Contributors'
project = u'connectomics'
copyright = u'2019-{}, {}'.format(datetime.datetime.now().year, author)

# 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 short X.Y version.
version = 'latest'
# The full version, including alpha/beta/rc tags.
release = 'latest'

# 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 = "en"

# 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.
# These patterns also affect html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# 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 = 'pytorch_sphinx_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_path = [pytorch_sphinx_theme.get_html_theme_path()]

html_theme_options = {
    'collapse_navigation': False,
    'display_version': True,
    'logo_only': True,
    'navigation_with_keys': True,
}

# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

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

# A shorter title for the navigation bar.  Default is the same as html_title.
#
html_short_title = "PyTC"

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
html_logo = '_templates/_static/img/logo.svg'

# 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 = '_templates/_static/img/favicon.svg'

# 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 = ["_templates/_static/"]
html_context = {"css_files": ["_static/css/pytc-theme.css",
                              "https://cdn.jsdelivr.net/npm/@docsearch/js@alpha",
                              "_static/css/readthedocs-doc-embed.css"
                              ]}
# 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 = []

# 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 = None

# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}

# 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 = True

# 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 = 'connectomicsdoc'

# -- 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, 'connectomics.tex', u'PyTorch Connectomics Documentation',
     author, 'manual'),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None

# 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 = []

# 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, 'connectomics', u'PyTorch Connectomics 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, 'connectomics', u'PyTorch Connectomics Documentation',
     author, 'connectomics', '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

# pdf_documents = [
#     ('index', u'connectomics', u'PyTorch Connectomics Documentation', author), ]


# def setup(app):
#     def skip(app, what, name, obj, skip, options):
#         members = [
#             '__init__',
#             '__repr__',
#             '__weakref__',
#             '__dict__',
#             '__module__',
#         ]
#         return True if name in members else skip

#     app.connect('autodoc-skip-member', skip)


# -- Extension configuration -------------------------------------------------

# -- Options for intersphinx extension ---------------------------------------

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
    "python": ("https://docs.python.org/3", None),
    "torch": ("https://pytorch.org/docs/stable/", None),
}

# -- Options for todo extension ----------------------------------------------

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

# -- Type hints configs ------------------------------------------------------

autodoc_inherit_docstrings = True
autoclass_content = "both"
autodoc_typehints = "description"
napoleon_attr_annotations = True

# -- A patch that turns-off cross refs for type annotations ------------------


# replaces pending_xref node with desc_type for type annotations
sphinx.domains.python.type_to_xref = lambda t, e=None: addnodes.desc_type(
    "", nodes.Text(t))

# -- Autosummary patch to get list of a classes, funcs automatically ----------


class BetterAutosummary(Autosummary):
    """Autosummary with autolisting for modules.

    By default it tries to import all public names (__all__),
    otherwise import all classes and/or functions in a module.

    Options:
    - :autolist: option to get list of classes and functions from currentmodule.
    - :autolist-classes: option to get list of classes from currentmodule.
    - :autolist-functions: option to get list of functions from currentmodule.

    Example Usage:

    .. currentmodule:: ignite.metrics

    .. autosummary::
        :nosignatures:
        :autolist:
    """

    # Add new option
    _option_spec = Autosummary.option_spec.copy()
    _option_spec.update(
        {
            "autolist": directives.unchanged,
            "autolist-classes": directives.unchanged,
            "autolist-functions": directives.unchanged,
        }
    )
    option_spec = _option_spec

    def run(self):
        for auto in ("autolist", "autolist-classes", "autolist-functions"):
            if auto in self.options:
                # Get current module name
                module_name = self.env.ref_context.get("py:module")
                # Import module
                module = import_module(module_name)

                # Get public names (if possible)
                try:
                    names = getattr(module, "__all__")
                except AttributeError:
                    # Get classes defined in the module
                    cls_names = [
                        name[0]
                        for name in getmembers(module, isclass)
                        if name[-1].__module__ == module_name and not (name[0].startswith("_"))
                    ]
                    # Get functions defined in the module
                    fn_names = [
                        name[0]
                        for name in getmembers(module, isfunction)
                        if (name[-1].__module__ == module_name) and not (name[0].startswith("_"))
                    ]
                    names = cls_names + fn_names
                    # It may happen that module doesn't have any defined class or func
                    if not names:
                        names = [name[0] for name in getmembers(module)]

                # Filter out members w/o doc strings
                names = [name for name in names if getattr(
                    module, name).__doc__ is not None]

                if auto == "autolist":
                    # Get list of all classes and functions inside module
                    names = [
                        name for name in names if (isclass(getattr(module, name)) or isfunction(getattr(module, name)))
                    ]
                else:
                    if auto == "autolist-classes":
                        # Get only classes
                        check = isclass
                    elif auto == "autolist-functions":
                        # Get only functions
                        check = isfunction
                    else:
                        raise NotImplementedError

                    names = [name for name in names if check(
                        getattr(module, name))]

                # Update content
                self.content = StringList(names)
        return super().run()


# Patch original Autosummary
sphinx.ext.autosummary.Autosummary = BetterAutosummary

# --- autosummary config -----------------------------------------------------
autosummary_generate = True

# --- nitpicky config : check internal links are correct or not --------------
nitpicky = True
# ignore links which can't be referenced
nitpick_ignore = [
    ("py:class", ".."),
    ("py:class", "TextIO"),
    ("py:class", "torch.device"),
    ("py:class", "_MpDeviceLoader"),
    ("py:class", "torch.nn.modules.module.Module"),
    ("py:class", "torch.optim.optimizer.Optimizer"),
    ("py:class", "torch.utils.data.dataset.Dataset"),
    ("py:class", "torch.utils.data.sampler.BatchSampler"),
    ("py:class", "torch.cuda.amp.grad_scaler.GradScaler"),
    ("py:class", "torch.optim.lr_scheduler._LRScheduler"),
    ("py:class", "torch.utils.data.dataloader.DataLoader"),
]