conf.py

from __future__ import annotations

import os
from datetime import UTC, datetime
from importlib.metadata import metadata
from types import MappingProxyType
from typing import TYPE_CHECKING, ClassVar

from docutils import nodes
from sphinx import addnodes
from sphinx.domains import Domain
from sphinx.errors import NoUri
from sphinx.ext.intersphinx import resolve_reference_in_inventory
from sphinx.util.docutils import SphinxDirective


if TYPE_CHECKING:
    from collections.abc import Mapping, Sequence

    from docutils.parsers.rst.states import Inliner
    from sphinx.application import Sphinx
    from sphinx.environment import BuildEnvironment


meta = metadata("scanpy-tutorials")
project = meta["Name"]
author = meta["Author"]
copyright = f"{datetime.now(UTC):%Y}, {author}"  # noqa: A001
release = version = meta["Version"]

extensions = ["myst_nb", "sphinx.ext.intersphinx", "sphinx_design"]
myst_enable_extensions = [
    "colon_fence",
]

templates_path = ["_templates"]
source_suffix = ".rst"
master_doc = "index"
language = "en"
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "scanpy_workshop", ".*cache"]
pygments_style = "sphinx"

intersphinx_mapping = dict(
    anndata=("https://anndata.readthedocs.io/en/stable/", None),
    scanpy=("https://scanpy.readthedocs.io/en/latest/", None),
)
suppress_warnings = ["image.not_readable"]

# -- Options for HTML output ----------------------------------------------

html_theme = "scanpydoc"
html_theme_options = dict(
    repository_url="https://github.com/theislab/scanpy-tutorials",
    repository_branch="master",
    use_repository_button=True,
)
html_static_path = ["_static"]
# include a warning background on RTD for everything but PR builds
html_css_files = (
    ["css/warning.css"]
    if os.environ.get("READTHEDOCS") and os.environ.get("READTHEDOCS_VERSION_TYPE") != "external"
    else []
)
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"

# -- Notebook settings ----------------------------------------------------

nb_execution_mode = "off"
nb_output_stderr = "remove"
myst_heading_anchors = 3
suppress_warnings = [
    # paga-paul15.ipynb: /_static/img/tutorials/paga_planaria.png
    "image.not_readable",
    # application/vnd.microsoft.datawrangler.viewer.v0+json
    "mystnb.unknown_mime_type",
]


# Roles “implementing” {cite}`…` and {cite:p}`…`/{cite:t}`…`


def fake_cite(
    name: str,
    rawtext: str,
    text: str,
    lineno: int,
    inliner: Inliner,
    options: Mapping[str, object] = MappingProxyType({}),
    content: Sequence[str] = (),
) -> tuple[list[nodes.Node], list[str]]:
    del name, lineno, options, content
    msg = f"cite:{text}"
    return [
        inliner.document.reporter.info(msg),
        nodes.emphasis(rawtext, f"[{text}]"),
    ], []


class FakeDomain(Domain):
    name: ClassVar = "cite"
    roles: ClassVar = dict(p=fake_cite, t=fake_cite)


# Role linking to the canonical location in scanpy’s docs


MSG = (
    "Please access this document in its canonical location as the currently accessed page may not be rendered correctly"
)


class CanonicalTutorial(SphinxDirective):
    required_arguments = 1
    has_content = False

    def run(self) -> list[nodes.Node]:
        """\
        Return a banner with a link to the canonical location.

        If the reference cannot be found, crash the build.
        """
        text = self.arguments[0]
        ref = resolve_reference_in_inventory(
            self.env,
            "scanpy",
            addnodes.pending_xref("", reftype="doc", refdomain="std", reftarget=text),
            nodes.inline("", text),
        )
        if ref is None:
            msg = f"Reference to scanpy:{text} not found"
            raise self.warning(msg)
        desc = nodes.inline("", f"{MSG}: ")
        banner = nodes.danger(
            text,
            nodes.paragraph("", "", desc, ref),
            classes=["admonition", "caution"],
        )
        return [banner]


def missing_reference(
    app: Sphinx,
    env: BuildEnvironment,
    node: addnodes.pending_xref,
    contnode: nodes.TextElement,
) -> nodes.Node | None:
    del app, env, contnode
    # ignore known scanpy labels
    if node["reftarget"] in {
        "external-data-integration",
        "eco-data-integration",
        "pl-embeddings",
    } or node["reftarget"].startswith("/tutorials"):
        raise NoUri
    return None


def setup(app: Sphinx) -> None:
    app.add_domain(FakeDomain)
    app.add_role("cite", fake_cite)
    app.add_directive("canonical-tutorial", CanonicalTutorial)
    app.connect("missing-reference", missing_reference)