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from __future__ import annotations
import sys
from datetime import datetime
from functools import partial
from importlib import metadata
from pathlib import Path, PurePosixPath
from typing import TYPE_CHECKING
from docutils import nodes
if TYPE_CHECKING:
from sphinx.application import Sphinx
HERE = Path(__file__).parent
_extension_dir = HERE / "extensions"
sys.path[:0] = [str(_extension_dir)]
# -- General configuration ------------------------------------------------
# General information
project = "anndata"
author = f"{project} developers"
copyright = f"{datetime.now():%Y}, scverse"
release = version = metadata.version("anndata")
# default settings
templates_path = ["_templates"]
html_static_path = ["_static"]
source_suffix = {".rst": "restructuredtext", ".md": "myst-nb"}
master_doc = "index"
default_role = "literal"
exclude_patterns = [
"_build",
"Thumbs.db",
".DS_Store",
"**.ipynb_checkpoints",
"tutorials/notebooks/*.rst",
# exclude all 0.x.y.md files, but not index.md
"release-notes/[!i]*.md",
"news.md", # is `include`d into index.md
]
pygments_style = "sphinx"
extensions = [
"myst_nb",
"sphinx_copybutton",
"sphinx.ext.autodoc",
"sphinx.ext.intersphinx",
"sphinx.ext.doctest",
"sphinx.ext.coverage",
"sphinx.ext.mathjax",
"sphinx.ext.napoleon",
"sphinx.ext.autosummary",
"sphinx_autodoc_typehints", # needs to be after napoleon
"sphinx_issues",
"sphinx_design",
"sphinxext.opengraph",
"scanpydoc", # needs to be before linkcode
"sphinx.ext.linkcode",
"IPython.sphinxext.ipython_console_highlighting",
"sphinx_toolbox.more_autodoc.autoprotocol",
*(p.stem for p in _extension_dir.glob("*.py")),
]
myst_enable_extensions = [
"html_image", # So README.md can be used on github and sphinx docs
"colon_fence",
"dollarmath",
]
myst_heading_anchors = 3
nb_execution_mode = "off"
# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
autodoc_mock_imports = ["torch"]
# autodoc_default_flags = ['members']
issues_github_path = "scverse/anndata"
rtd_links_prefix = PurePosixPath("src")
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [("Params", "Parameters")]
typehints_defaults = "braces"
todo_include_todos = False
nitpicky = True # Report broken links
nitpick_ignore = [ # APIs without an intersphinx entry
# This API isn’t actually documented
("py:class", "anndata._core.raw.Raw"),
# TODO: remove zappy support; the zappy repo is archived
("py:class", "anndata.compat.ZappyArray"),
]
def setup(app: Sphinx):
app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
# TODO: move to scanpydoc
if TYPE_CHECKING:
from docutils.nodes import TextElement, reference
from sphinx.addnodes import pending_xref
from sphinx.environment import BuildEnvironment
def res(
app: Sphinx, env: BuildEnvironment, node: pending_xref, contnode: TextElement
) -> reference | None:
return env.domains["py"].resolve_xref(
env,
node["refdoc"],
app.builder,
node["reftype"],
node["reftarget"],
node,
contnode,
)
app.connect("missing-reference", res, priority=502)
intersphinx_mapping = dict(
awkward=("https://awkward-array.org/doc/stable", None),
cupy=("https://docs.cupy.dev/en/stable", None),
dask=("https://docs.dask.org/en/stable", None),
fsspec=("https://filesystem-spec.readthedocs.io/en/stable/", None),
h5py=("https://docs.h5py.org/en/latest", None),
hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest", None),
kvikio=("https://docs.rapids.ai/api/kvikio/stable/", None),
loompy=("https://linnarssonlab.org/loompy", None),
numpy=("https://numpy.org/doc/stable", None),
obstore=("https://developmentseed.org/obstore/latest/", None),
pandas=("https://pandas.pydata.org/pandas-docs/stable", None),
# TODO: switch to `/3` once docs are built with Python 3.14
# https://github.com/readthedocs/readthedocs.org/issues/12523
python=("https://docs.python.org/3.13", None),
scipy=("https://docs.scipy.org/doc/scipy", None),
sklearn=("https://scikit-learn.org/stable", None),
xarray=("https://docs.xarray.dev/en/stable", None),
zarr=("https://zarr.readthedocs.io/en/stable/", None),
zarrs=("https://zarrs-python.readthedocs.io/en/stable/", None),
)
qualname_overrides = {
"h5py._hl.group.Group": "h5py.Group",
"h5py._hl.files.File": "h5py.File",
"h5py._hl.dataset.Dataset": "h5py.Dataset",
"anndata._core.anndata.AnnData": "anndata.AnnData",
**{
f"anndata._core.aligned_mapping.{cls}{kind}": "collections.abc.Mapping"
for cls in ["Layers", "AxisArrays", "PairwiseArrays"]
for kind in ["", "View"]
},
"anndata._types.ReadCallback": "anndata.experimental.ReadCallback",
"anndata._types.WriteCallback": "anndata.experimental.WriteCallback",
"anndata._types.Read": "anndata.experimental.Read",
"anndata._types.Write": "anndata.experimental.Write",
"anndata._types.Dataset2DIlocIndexer": "anndata.experimental.Dataset2DIlocIndexer",
"zarr.core.array.Array": "zarr.Array",
"zarr.core.group.Group": "zarr.Group",
# Buffer is not yet exported, so the buffer class registry is the closest thing
"zarr.core.buffer.core.Buffer": "zarr.registry.Registry",
"zarr.storage._common.StorePath": "zarr.storage.StorePath",
"anndata.compat.DaskArray": "dask.array.Array",
"anndata.compat.CupyArray": "cupy.ndarray",
"anndata.compat.CupySparseMatrix": "cupyx.scipy.sparse.spmatrix",
"anndata.compat.XDataArray": "xarray.DataArray",
"anndata.compat.XDataset": "xarray.Dataset",
"awkward.highlevel.Array": "ak.Array",
"numpy.int64": ("py:attr", "numpy.int64"),
"pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"),
"pandas.DataFrame.loc": ("py:attr", "pandas.DataFrame.loc"),
# should be fixed soon: https://github.com/tox-dev/sphinx-autodoc-typehints/pull/516
"types.EllipsisType": ("py:data", "types.EllipsisType"),
"pathlib._local.Path": "pathlib.Path",
}
autodoc_type_aliases = dict(
NDArray=":data:`~numpy.typing.NDArray`",
AxisStorable=":data:`~anndata.typing.AxisStorable`",
**{
f"{v}variantRWAble": ":data:`~anndata.typing.RWAble`"
for v in ["In", "Co", "Contra"]
},
)
# -- Social cards ---------------------------------------------------------
ogp_site_url = "https://anndata.readthedocs.io/"
ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg"
# -- Options for HTML output ----------------------------------------------
# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = dict(
use_repository_button=True,
repository_url="https://github.com/scverse/anndata",
repository_branch="main",
navigation_with_keys=False, # https://github.com/pydata/pydata-sphinx-theme/issues/1492
)
html_logo = "_static/img/anndata_schema.svg"
issues_github_path = "scverse/anndata"
html_show_sphinx = False
# -- Options for other output formats ------------------------------------------
htmlhelp_basename = f"{project}doc"
doc_title = f"{project} Documentation"
latex_documents = [(master_doc, f"{project}.tex", doc_title, author, "manual")]
man_pages = [(master_doc, project, doc_title, [author], 1)]
texinfo_documents = [
(
master_doc,
project,
doc_title,
author,
project,
"One line description of project.",
"Miscellaneous",
)
]
|
