[pre-commit.ci] pre-commit autoupdate (#529)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.5.6](astral-sh/ruff-pre-commit@v0.5.1...v0.5.6)

* Update conf.py

* Exclude sphinx 7.4

* Fix rtd

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Gregor Sturm <[email protected]>

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
       - id: prettier
         exclude: '^\.conda'
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.1
+    rev: v0.5.6
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

docs/conf.py

@@ -10,6 +10,8 @@
 from importlib.metadata import metadata
 from pathlib import Path
 
+import os
+
 
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE / "extensions"))
@@ -45,6 +47,12 @@
     "conf_py_path": "/docs/",  # Path in the checkout to the docs root
 }
 
+# Set canonical URL from the Read the Docs Domain
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+# Tell Jinja2 templates the build is running on Read the Docs
+if os.environ.get("READTHEDOCS", "") == "True":
+    html_context["READTHEDOCS"] = True
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings.
@@ -96,25 +104,25 @@
 }
 
 intersphinx_mapping = {
-    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
-    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
-    "h5py": ("https://docs.h5py.org/en/stable/", None),
-    "cycler": ("https://matplotlib.org/cycler/", None),
-    "ipython": ("https://ipython.readthedocs.io/en/stable/", None),
-    "leidenalg": ("https://leidenalg.readthedocs.io/en/latest/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable", None),
+    "h5py": ("https://docs.h5py.org/en/stable", None),
+    "cycler": ("https://matplotlib.org/cycler", None),
+    "ipython": ("https://ipython.readthedocs.io/en/stable", None),
+    "leidenalg": ("https://leidenalg.readthedocs.io/en/latest", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "python": ("https://docs.python.org/3", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
-    "seaborn": ("https://seaborn.pydata.org/", None),
-    "sklearn": ("https://scikit-learn.org/stable/", None),
-    "networkx": ("https://networkx.org/documentation/networkx-1.10/", None),
-    "dandelion": ("https://sc-dandelion.readthedocs.io/en/latest/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "seaborn": ("https://seaborn.pydata.org", None),
+    "sklearn": ("https://scikit-learn.org/stable", None),
+    "networkx": ("https://networkx.org/documentation/networkx-1.10", None),
+    "dandelion": ("https://sc-dandelion.readthedocs.io/en/latest", None),
     "muon": ("https://muon.readthedocs.io/en/latest", None),
-    "mudata": ("https://mudata.readthedocs.io/en/latest/", None),
-    "awkward": ("https://awkward-array.org/doc/main/", None),
-    "pooch": ("https://www.fatiando.org/pooch/latest/", None),
+    "mudata": ("https://mudata.readthedocs.io/en/latest", None),
+    "awkward": ("https://awkward-array.org/doc/main", None),
+    "pooch": ("https://www.fatiando.org/pooch/latest", None),
     "joblib": ("https://joblib.readthedocs.io/en/latest", None),
 }
 

pyproject.toml

@@ -50,7 +50,7 @@ dev = [
 ]
 doc = [
     "docutils>=0.8,!=0.18.*,!=0.19.*",
-    'sphinx>=4',
+    'sphinx>=7,<7.4', # https://github.com/sphinx-doc/sphinx/issues/12589
     "sphinx-book-theme>=1.0.0",
     "myst-nb>=1.1.0",
     'sphinxcontrib-bibtex>=1.0.0',