Backport PR #3959 on branch 1.12.x (ci: write zarr 3 format with supported anndata versions) (#3961)

Co-authored-by: Philipp A <flying-sheep@web.de>

Author: meeseeksmachine

hatch.toml

@@ -4,7 +4,11 @@ dependency-groups = [ "dev" ]
 
 [envs.docs]
 dependency-groups = [ "doc" ]
-extra-dependencies = [ "pandas>=3" ]
+# MyST-NB 1.3.0 spams the doc build logs making debugging hard, so use https://github.com/executablebooks/MyST-NB/pull/704
+extra-dependencies = [
+    "pandas>=3",
+    "myst-nb @ git+https://github.com/executablebooks/MyST-NB.git@91273a686c66fd0383466c80eede61b208d7e426",
+]
 scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"

pyproject.toml

@@ -111,7 +111,7 @@ test = [
     "scanpy[plotting]",
 ]
 doc = [
-    "sphinx>=8.2.3",
+    "sphinx>=9.1.0",
     "sphinx-book-theme>=1.1.0",
     "scanpydoc>=0.16.1",
     "sphinx-autodoc-typehints>=1.25.2",
@@ -198,6 +198,8 @@ filterwarnings = [
     "ignore:.*'(parseAll)'.*'(parse_all)':DeprecationWarning",
     # igraph vs leidenalg warning
     "ignore:The `igraph` implementation of leiden clustering:UserWarning",
+    # everybody uses this zarr 3 feature, including us, XArray, lots of data out there …
+    "ignore:Consolidated metadata is currently not part:UserWarning",
 ]
 
 [tool.coverage.run]

src/testing/scanpy/_pytest/__init__.py

@@ -8,6 +8,7 @@
 from typing import TYPE_CHECKING
 
 import pytest
+from packaging.version import Version
 
 from .fixtures import *  # noqa: F403
 from .marks import needs
@@ -28,17 +29,21 @@ def original_settings(
 ) -> Generator[Mapping[str, object], None, None]:
     """Switch to agg backend, reset settings, and close all figures at teardown."""
     # make sure seaborn is imported and did its thing
+    import anndata as ad
     import seaborn as sns  # noqa: F401
     from matplotlib import pyplot as plt
     from matplotlib.testing import setup
 
     import scanpy as sc
+    from scanpy._compat import pkg_version
 
     global _original_settings  # noqa: PLW0603
     if _original_settings is None:
         _original_settings = MappingProxyType(sc.settings.__dict__.copy())
 
     setup()
+    if pkg_version("anndata") >= Version("0.12"):
+        ad.settings.zarr_write_format = 3  # default in anndata 0.13, warns otherwise
     sc.settings.logfile = sys.stderr
     sc.settings.verbosity = "hint"
     sc.settings.autoshow = True