(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. <[email protected]>
scverse · Jan 10, 2025 · 1bf63a0 · 1bf63a0
1 parent a8c62e8
commit 1bf63a0
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 4 deletions.
diff --git a/benchmarks/asv.conf.json b/benchmarks/asv.conf.json
@@ -79,7 +79,7 @@
         "natsort": [""],
         "pandas": [""],
         "memory_profiler": [""],
-        "zarr": [""],
+        "zarr": ["2.18.4"],
         "pytoml": [""],
         "pytest": [""],
         "pooch": [""],

diff --git a/docs/conf.py b/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),
 )

diff --git a/docs/release-notes/1819.bugfix.md b/docs/release-notes/1819.bugfix.md
@@ -0,0 +1 @@
+Upper bound `zarr` at runtime {user}`ilan-gold`
diff --git a/pyproject.toml b/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",

diff --git a/src/anndata/compat/__init__.py b/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:
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Upper bound `zarr` at runtime {user}`ilan-gold`