(fix): upper bound zarr at runtime (and in docs + benchmark) (#1819)

* (fix): upper bound zarr at runtime

* (chore): improve message

* (fix): asv benchmarking config

* (chore): fix docs

* (fix): intersphinx mapping

* (chore): release note

* simpler version

* (refactor): `ImportError` instead of `RuntimeError`

---------

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

Author: ilan-gold

benchmarks/asv.conf.json

@@ -79,7 +79,7 @@
         "natsort": [""],
         "pandas": [""],
         "memory_profiler": [""],
-        "zarr": [""],
+        "zarr": ["2.18.4"],
         "pytoml": [""],
         "pytest": [""],
         "pooch": [""],

docs/conf.py

@@ -132,7 +132,7 @@ def setup(app: Sphinx):
     python=("https://docs.python.org/3", None),
     scipy=("https://docs.scipy.org/doc/scipy", None),
     sklearn=("https://scikit-learn.org/stable", None),
-    zarr=("https://zarr.readthedocs.io/en/stable", None),
+    zarr=("https://zarr.readthedocs.io/en/v2.18.4/", None),
     xarray=("https://docs.xarray.dev/en/stable", None),
     dask=("https://docs.dask.org/en/stable", None),
 )

docs/release-notes/1819.bugfix.md

@@ -0,0 +1 @@
+Upper bound `zarr` at runtime {user}`ilan-gold`

pyproject.toml

@@ -74,7 +74,7 @@ doc = [
     "sphinxext.opengraph",
     "nbsphinx",
     "scanpydoc[theme,typehints] >=0.14.1",
-    "zarr",
+    "zarr<3",
     "awkward>=2.3",
     "IPython",                          # For syntax highlighting in notebooks
     "myst_parser",
@@ -88,7 +88,7 @@ test = [
     "loompy>=3.0.5",
     "pytest>=8.2,<8.3.4",
     "pytest-cov>=2.10",
-    "zarr<3.0.0a0",
+    "zarr<3",
     "matplotlib",
     "scikit-learn",
     "openpyxl",

src/anndata/compat/__init__.py

@@ -91,6 +91,11 @@ def __exit__(self, *_exc_info) -> None:
 #############################
 
 if find_spec("zarr") or TYPE_CHECKING:
+    import zarr
+
+    if Version(zarr.__version__).major > 2:
+        raise ImportError("zarr-python major version > 2 is not supported")
+
     from zarr.core import Array as ZarrArray
     from zarr.hierarchy import Group as ZarrGroup
 else: