Intron7 · Oct 26, 2026 · Oct 26, 2026 · Oct 26, 2026 · Oct 26, 2026 · Oct 26, 2026
diff --git a/docs/_static/css/override.css b/docs/_static/css/override.css
@@ -19,14 +19,8 @@ dl.citation > dt {
 	font-size: 70% !important;
 }
 
-/* RSC colors are
-#7400ff - violet
-#76b900 - green
-#4169e1 - blue
-*/
-
-p.caption .caption-text {
-    color: #7400ff;
-    font-weight: 600;
-    text-transform: uppercase;
+/* scverse-doc mixes the link hover colour towards the (near-white) text colour,
+   which greys out the accent in dark mode. Brighten it instead, keeping chroma and hue. */
+html[data-theme="dark"] {
+	--pst-color-primary-highlight: oklch(from var(--scverse-color-accent-text) calc(l + 0.08) c h);
 }
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -2,15 +2,16 @@
 
 # -- Path setup --------------------------------------------------------------
 import sys
-import os
 from datetime import datetime
 from importlib.metadata import metadata
-from pathlib import Path, PurePosixPath
+from pathlib import Path
 from typing import TYPE_CHECKING
 import anndata  # noqa
 import fast_array_utils  # noqa
 from docutils import nodes
 from docutils.parsers.rst import roles
+from scverse_doc.config import DEFAULTS
+from scverse_doc.registry import intersphinx
 
 if TYPE_CHECKING:
     from sphinx.application import Sphinx
@@ -19,9 +20,6 @@
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE.parent / "src/"))
 
-on_rtd = os.environ.get("READTHEDOCS") == "True"
-rtd_links_prefix = PurePosixPath("src")
-
 # -- Project information -----------------------------------------------------
 
 info = metadata("rapids_singlecell")
@@ -31,15 +29,13 @@
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}"
 version = info["Version"]
-repository_url = "https://github.com/scverse/rapids-singlecell"
+source_repository = "https://github.com/scverse/rapids-singlecell"
 
 # The full version, including alpha/beta/rc tags
 release = info["Version"]
 
 templates_path = ["_templates"]
 bibtex_bibfiles = ["references.bib"]
-nitpicky = True  # Warn about broken links
-needs_sphinx = "4.5"
 suppress_warnings = [
     "ref.citation",
     "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
@@ -48,30 +44,20 @@
 # -- General configuration ---------------------------------------------------
 
 extensions = [
-    "myst_nb",
-    "sphinx_design",
-    "sphinx.ext.autodoc",
+    "scverse_doc",  # sets up napoleon, so needs to be before sphinx_autodoc_typehints
     "sphinx.ext.doctest",
     "sphinx.ext.coverage",
     "sphinx.ext.mathjax",
-    "sphinx.ext.autosummary",
-    "sphinx.ext.napoleon",
-    "sphinx.ext.intersphinx",
     "sphinx.ext.githubpages",
     "sphinx_autodoc_typehints",
     "sphinx.ext.extlinks",
     "sphinx.ext.imgconverter",
-    "sphinx_copybutton",
     "nbsphinx",
-    "scanpydoc",
     "scverse_misc.sphinx_ext",
     "sphinx.ext.linkcode",
-    "sphinx_tabs.tabs",
-    "sphinxext.opengraph",
     "sphinxcontrib.bibtex",
 ]
 
-autosummary_generate = True
 autodoc_member_order = "bysource"
 autodoc_mock_imports = [
     "cudf",
@@ -82,49 +68,18 @@
     "pylibraft",
     "cuvs",
 ]
-default_role = "literal"
-napoleon_google_docstring = False
-napoleon_numpy_docstring = True
-napoleon_include_init_with_doc = False
 napoleon_use_rtype = False  # having a separate entry generally helps readability
-napoleon_use_param = True
 api_dir = HERE / "api"
-myst_enable_extensions = [
-    "amsmath",
-    "colon_fence",
-    "deflist",
-    "dollarmath",
-    "html_image",
-    "html_admonition",
-]
 myst_url_schemes = ("http", "https", "mailto", "ftp")
-nb_output_stderr = "remove"
-nb_execution_mode = "off"
-nb_merge_streams = True
 typehints_defaults = "braces"
 
-source_suffix = {
-    ".rst": "restructuredtext",
-    ".ipynb": "myst-nb",
-    ".myst": "myst-nb",
-}
-
-intersphinx_mapping = {
-    "anndata": ("https://anndata.scverse.org/en/stable/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+# scverse core packages, Python, NumPy, SciPy, pandas and Matplotlib come from the registry
+intersphinx_mapping = intersphinx("squidpy", "spatialdata", "pertpy", "decoupler") | {
     "cupy": ("https://docs.cupy.dev/en/stable/", None),
-    "python": ("https://docs.python.org/3", None),
     "cuml": ("https://docs.rapids.ai/api/cuml/stable/", None),
-    "pandas": ("https://pandas.pydata.org/docs/", None),
     "cudf": ("https://docs.rapids.ai/api/cudf/stable/", None),
     "cugraph": ("https://docs.rapids.ai/api/cugraph/stable/", None),
-    "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
-    "squidpy": ("https://squidpy.readthedocs.io/en/stable/", None),
-    "spatialdata": ("https://spatialdata.scverse.org/en/stable/", None),
-    "pertpy": ("https://pertpy.scverse.org/en/stable/", None),
     "seaborn": ("https://seaborn.pydata.org/", None),
-    "decoupler": ("https://decoupler.readthedocs.io/en/latest/", None),
     "rmm": ("https://docs.rapids.ai/api/rmm/stable/", None),
     "statsmodels": ("https://www.statsmodels.org/stable/", None),
     "omnipath": ("https://omnipath.readthedocs.io/en/latest/", None),
@@ -135,11 +90,8 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    "_build",
-    "Thumbs.db",
-    ".DS_Store",
+    *DEFAULTS.exclude_patterns,
     "._*",
-    "*.ipynb_checkpoints",
     "release-notes/blank.md",
 ]
 
@@ -158,32 +110,24 @@
 
 # -- Options for HTML output -------------------------------------------------
 
-html_theme = "scanpydoc"
 html_theme_options = {
-    "repository_url": repository_url,
-    "repository_branch": os.environ.get("READTHEDOCS_GIT_IDENTIFIER", "main"),
-    "use_repository_button": True,
+    # TODO: drop once scverse-doc is released with the website accents (scverse/scverse-doc#78)
+    "accent": "#76b900",  # NVIDIA green
+    "secondary_accent": "#7400ff",  # violet, used for the sidebar captions
     "navigation_with_keys": False,
     "show_toc_level": 2,
 }
 html_show_sphinx = False
 html_logo = "_static/logo_RTD.svg"
 html_static_path = ["_static"]
 html_css_files = ["css/override.css"]
-html_title = "rapids-singlecell"
 
 # OpenGraph metadata for social media previews
 ogp_site_url = "https://rapids-singlecell.readthedocs.io/"
 ogp_site_name = "rapids-singlecell"
 ogp_image = "_static/logo_RTD.svg"
 
-qualname_overrides = {
-    "numpy.bool_": "numpy.bool",  # Since numpy 2, numpy.bool is the canonical dtype
-    # Since numpy 2.5, NDArray is a TypeAliasType defined in numpy._typing._array_like,
-    # so a subscripted NDArray[...] reports that private module and sphinx-autodoc-typehints
-    # builds the target as <annotation module>.<type qualname> -- a name numpy does not
-    # document. Same treatment as anndata gives the pre-2.5 spelling of this alias.
-    "numpy._typing._array_like.GenericAlias": ("py:data", "numpy.typing.NDArray"),
+xref_overrides = {
     "spatialdata._core.spatialdata.SpatialData": "spatialdata.SpatialData",
 }
 
@@ -215,17 +159,6 @@ def setup(app: Sphinx) -> None:
     """App setup hook."""
     app.add_role("small", roles.GenericRole("small", nodes.inline))
     app.add_role("smaller", roles.GenericRole("smaller", nodes.inline))
-    app.add_config_value(
-        "recommonmark_config",
-        default={
-            "auto_toc_tree_section": "Contents",
-            "enable_auto_toc_tree": True,
-            "enable_math": True,
-            "enable_inline_math": False,
-            "enable_eval_rst": True,
-        },
-        rebuild=True,
-    )
 
 
 # extlinks config

diff --git a/docs/release-notes/0.19.0.md b/docs/release-notes/0.19.0.md
@@ -0,0 +1,5 @@
+### 0.19.0 {small}`the-future`
+
+```{rubric} Misc
+```
+* Switch the documentation theme from `scanpydoc` to the shared scverse theme `scverse-doc` {pr}`856` {smaller}`S Dicks`
diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md
@@ -2,6 +2,10 @@
 
 # Release notes
 
+## Version 0.19.0
+```{include} /release-notes/0.19.0.md
+```
+
 ## Version 0.18.0
 ```{include} /release-notes/0.18.1.md
 ```

diff --git a/pyproject.toml b/pyproject.toml
@@ -52,15 +52,11 @@ rapids-cu12 = [
 
 [dependency-groups]
 docs = [
-    "sphinx>=4.5.0",
-    "sphinx-copybutton",
+    "sphinx>=8.1",
     "nbsphinx>=0.8.12",
-    "myst-nb",
-    "sphinx-design",
-    "sphinx-tabs",
-    "sphinxext-opengraph",
     "sphinxcontrib.bibtex",
-    "scanpydoc[typehints,theme]>=0.9.4",
+    "scverse-doc[full]>=0.3",
+    "sphinx-autodoc-typehints",
     "scverse-misc[sphinx]>=0.1.3",
     "dask",
     "pytest",