Update instance repo (PR 582 -- feat: switch to scverse-doc)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "8c6abe9294f083e19c990f9c8e79d82b0eecbc8d",
+  "commit": "27f1e4abced9f9b7c557955c3c8ac3344fb542a6",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -37,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "8c6abe9294f083e19c990f9c8e79d82b0eecbc8d"
+      "_commit": "27f1e4abced9f9b7c557955c3c8ac3344fb542a6"
     }
   },
   "directory": null

.readthedocs.yaml

@@ -4,7 +4,6 @@ build:
   os: ubuntu-24.04
   tools:
     python: "3.14"
-    nodejs: latest
   jobs:
     create_environment:
       - asdf plugin add uv

biome.jsonc

@@ -2,6 +2,7 @@
     "$schema": "https://biomejs.dev/schemas/2.6.3/schema.json",
     "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
+    "markdown": { "parser": { "frontmatter": true } },
     "overrides": [
         {
             "includes": ["./.vscode/*.json", "**/*.jsonc"],

docs/conf.py

@@ -1,137 +1,38 @@
 # Configuration file for the Sphinx documentation builder.
+# `scverse_doc` sets the theme and shared defaults, see https://scverse-doc.readthedocs.io
+# For the full list of options, see https://www.sphinx-doc.org/page/usage/configuration.html
 
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/page/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-import shutil
-import sys
 from datetime import datetime
 from importlib.metadata import metadata
-from pathlib import Path
-
-from sphinxcontrib import katex
-
-HERE = Path(__file__).parent
-sys.path.insert(0, str(HERE / "extensions"))
-
-
-# -- Project information -----------------------------------------------------
 
 # NOTE: If you installed your project in editable mode, this might be stale.
 #       If this is the case, reinstall it to refresh the metadata
 info = metadata("cookiecutter-scverse-instance")
 project = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
-version = info["Version"]
+version = release = info["Version"]
 urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
-repository_url = urls["Source"]
-
-# The full version, including alpha/beta/rc tags
-release = info["Version"]
+source_repository = urls["Source"]
 
-bibtex_bibfiles = ["references.bib"]
-templates_path = ["_templates"]
-nitpicky = True  # Warn about broken links
-needs_sphinx = "4.0"
-
-html_context = {
-    "display_github": True,  # Integrate GitHub
-    "github_user": "scverse",
-    "github_repo": project,
-    "github_version": "main",
-    "conf_py_path": "/docs/",
-}
-
-# -- 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 = [
-    "myst_nb",
-    "sphinx_copybutton",
-    "sphinx.ext.autodoc",
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.autosummary",
-    "sphinx.ext.napoleon",
+    "scverse_doc",
+    "scverse_misc.sphinx_ext",
     "sphinxcontrib.bibtex",
-    "sphinxcontrib.katex",
     "sphinx_autodoc_typehints",
-    "sphinx_design",
     "IPython.sphinxext.ipython_console_highlighting",
-    "sphinxext.opengraph",
-    "scverse_misc.sphinx_ext",
-    *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
-autosummary_generate = True
-autodoc_member_order = "groupwise"
-default_role = "literal"
-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
-myst_heading_anchors = 6  # create anchors for h1-h6
-myst_enable_extensions = [
-    "amsmath",
-    "colon_fence",
-    "deflist",
-    "dollarmath",
-    "html_image",
-    "html_admonition",
-]
-myst_url_schemes = ("http", "https", "mailto")
-nb_output_stderr = "remove"
-nb_execution_mode = "off"
-nb_merge_streams = True
+bibtex_bibfiles = ["references.bib"]
 typehints_defaults = "braces"
 always_use_bars_union = True  # use `|` instead of `Union` in types even when building with Python ≤3.14
 
-source_suffix = {
-    ".rst": "restructuredtext",
-    ".ipynb": "myst-nb",
-    ".myst": "myst-nb",
-}
-
-intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
-    "anndata": ("https://anndata.scverse.org/en/stable/", None),
-    "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-}
-
-# List of patterns, relative to source directory, that match files and
-# 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", "**.ipynb_checkpoints"]
-
-
-# -- 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 = "sphinx_book_theme"
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
 
-html_title = project
-
-html_theme_options = {
-    "repository_url": repository_url,
-    "use_repository_button": True,
-    "path_to_docs": "docs/",
-    "navigation_with_keys": False,
+xref_overrides = {
+    # If building the documentation fails because a type annotation links to a private path
+    # (e.g. `igraph._igraph.GraphBase`), map it to the documented name here.
+    # For a missing link that can’t be fixed this way, add it to `nitpick_ignore` instead.
+    #     "igraph._igraph.GraphBase": "igraph.GraphBase",
 }
-
-pygments_style = "default"
-katex_prerender = shutil.which(katex.NODEJS_BINARY) is not None
-
-nitpick_ignore = [
-    # If building the documentation fails because of a missing link that is outside your control,
-    # you can add an exception to this list.
-    #     ("py:class", "igraph.Graph"),
-]

pyproject.toml

@@ -45,17 +45,11 @@ test = [
 doc = [
   "ipykernel",
   "ipython",
-  "myst-nb>=1.1",
   "pandas",
-  "scverse-misc[sphinx]>=0.1.2",
-  "sphinx>=8.1",
+  "scverse-doc[full]>=0.5",
+  "scverse-misc[sphinx]>=0.1.8",
   "sphinx-autodoc-typehints",
-  "sphinx-book-theme>=1",
-  "sphinx-copybutton",
-  "sphinx-design",
   "sphinxcontrib-bibtex>=1",
-  "sphinxcontrib-katex",
-  "sphinxext-opengraph",
 ]
 typecheck = [
   "mypy",