# 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 --------------------------------------------------------------

import sys

from datetime import datetime

from pathlib import Path

# 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 moscot

sys.path.insert(0, str(Path(__file__).parent / "extensions"))

# -- Project information -----------------------------------------------------

project = moscot.__name__

author = moscot.__author__

version = moscot.__version__

copyright = f"{datetime.now():%Y}, Theislab"

# -- 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 = [

    "sphinx.ext.autodoc",

    "sphinx.ext.napoleon",

    "sphinx.ext.viewcode",

    "sphinx.ext.mathjax",

    "sphinx.ext.intersphinx",

    "sphinx.ext.autosummary",

    "sphinxcontrib.bibtex",

    "sphinx_copybutton",

    "sphinx_autodoc_typehints",

    "myst_nb",

    "sphinx_design",  # for cards

    "sphinx_tippy",

    "typed_returns",

]

intersphinx_mapping = {

    "python": ("https://docs.python.org/3", None),

    "numpy": ("https://numpy.org/doc/stable/", None),

    "scipy": ("https://docs.scipy.org/doc/scipy/", None),

    "pandas": ("https://pandas.pydata.org/docs/", None),

    "networkx": ("https://networkx.org/documentation/stable/", None),

    "jax": ("https://jax.readthedocs.io/en/latest/", None),

    "ott": ("https://ott-jax.readthedocs.io/en/latest/", None),

    "matplotlib": ("https://matplotlib.org/stable/", None),

    "anndata": ("https://anndata.readthedocs.io/en/latest/", None),

    "scanpy": ("https://scanpy.readthedocs.io/en/latest/", None),

    "squidpy": ("https://squidpy.readthedocs.io/en/latest/", None),

    "mudata": ("https://mudata.readthedocs.io/en/latest/", None),

}

master_doc = "index"

pygments_style = "tango"

pygments_dark_style = "monokai"

nitpicky = True

nitpick_ignore = [

    ("py:class", "numpy.float64"),

    # see: https://github.com/numpy/numpydoc/issues/275

    ("py:class", "None.  Remove all items from D."),

    ("py:class", "a set-like object providing a view on D's items"),

    ("py:class", "a set-like object providing a view on D's keys"),

    ("py:class", "v, remove specified key and return the corresponding value."),  # noqa: E501

    ("py:class", "None.  Update D from dict/iterable E and F."),

    ("py:class", "an object providing a view on D's values"),

    ("py:class", "a shallow copy of D"),

    # ignore these classes until ott-jax adds them to their docs

    ("py:class", "ott.initializers.quadratic.initializers.BaseQuadraticInitializer"),

    ("py:class", "ott.initializers.linear.initializers.SinkhornInitializer"),

]

# TODO(michalk8): remove once typing has been cleaned-up

nitpick_ignore_regex = [

    (r"py:class", r"moscot\..*(K|B|O)"),

    (r"py:class", r"numpy\._typing.*"),

    (r"py:class", r"moscot\..*Protocol.*"),

    (

        r"py:class",

        r"moscot.base.output.BaseSolverOutput",

    ),  # https://github.com/sphinx-doc/sphinx/issues/10974 means there is simply no way around this with generics

]

# bibliography

bibtex_bibfiles = ["references.bib"]

bibtex_reference_style = "author_year"

bibtex_default_style = "alpha"

# Add any paths that contain templates here, relative to this directory.

templates_path = ["_templates"]

source_suffix = {

    ".rst": "restructuredtext",

    ".ipynb": "myst-nb",

}

# myst

nb_execution_mode = "off"

myst_enable_extensions = [

    "colon_fence",

    "dollarmath",

    "amsmath",

]

myst_heading_anchors = 3

# autodoc + napoleon

autosummary_generate = True

autodoc_member_order = "alphabetical"

autodoc_typehints = "description"

napoleon_google_docstring = False

napoleon_numpy_docstring = True

# spelling

spelling_lang = "en_US"

spelling_warning = True

spelling_word_list_filename = "spelling_wordlist.txt"

spelling_add_pypi_package_names = True

spelling_exclude_patterns = ["references.rst"]

# see: https://pyenchant.github.io/pyenchant/api/enchant.tokenize.html

spelling_filters = [

    "enchant.tokenize.URLFilter",

    "enchant.tokenize.EmailFilter",

    "enchant.tokenize.MentionFilter",

]

# hover

tippy_anchor_parent_selector = "div.content"

tippy_enable_mathjax = True

# no need because of sphinxcontrib-bibtex

tippy_enable_doitips = False

linkcheck_report_timeouts_as_broken = True

linkcheck_ignore = [

    # 403 Client Error

    r"https://doi.org/10.1126/science.aad0501",

    r"https://resources.aertslab.org/cistarget/tf_lists/",

    r"https://doi.org/10.1126/science.aax1971",

    r"https://doi.org/10.1093/nar/gkac235",

    r"https://www.science.org/doi/abs/10.1126/science.aax1971",

    r"https://doi.org/10.1101/2022.01.10.475692",

    r"https://www.biorxiv.org/content/10.1101/2023.04.14.536867v1",

    r"https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2",

    r"https://www.biorxiv.org/content/early/2022/01/11/2022.01.10.475692",

    r"https://doi.org/10.1145/2516971.2516977",

    r"https://doi.org/10.3390/a13090212",

    r"https://www.mdpi.com/1999-4893/13/9/212",

]

exclude_patterns = ["_build", "**.ipynb_checkpoints", "notebooks/README.rst", "notebooks/CONTRIBUTING.rst"]

# -- 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 = "furo"

html_static_path = ["_static"]

html_css_files = [

    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css",

]

html_show_sphinx = False

html_show_sourcelink = False

html_theme_options = {

    "sidebar_hide_name": True,

    "light_logo": "img/light_mode_logo.png",

    "dark_logo": "img/dark_mode_logo.png",

    "light_css_variables": {

        "color-brand-primary": "#003262",

        "color-brand-content": "#003262",

        "admonition-font-size": "var(--font-size-normal)",

        "admonition-title-font-size": "var(--font-size-normal)",

        "code-font-size": "var(--font-size--small)",

    },

    "footer_icons": [

        {

            "name": "GitHub",

            "url": "https://github.com/theislab/moscot",

            "html": "",

            "class": "fab fa-github",

        },

    ],

}