fix: ad.settings.override order for sharding

docs/release-notes/0.12.4.md

@@ -1,4 +1,6 @@
 (v0.12.4)=
 ### 0.12.4 {small}`2025-10-27`
 
-No significant changes.
+#### Bug fixes
+
+- {func}`dask.array.store` was producing corrupted data with zarr v3 + distributed scheduler + a lock (which we used internally): see {issue}`dask/dask#12109`. Thus dense arrays were potentially being stored with corrupted data. The solution is to remove the lock for newer versions of dask but without the lock in older versions, it is impossible to store the data. Thus versions of dask older than `2025.4.0` will not be supported for writing dense data. {user}`ilan-gold`

docs/release-notes/2342.fix.md

@@ -0,0 +1 @@
+{attr}`anndata.settings.zarr_write_format` and {attr}`anndata.settings.auto_shard_zarr_v3` can now be set together {user}`ilan-gold`

src/anndata/_settings.py

@@ -368,15 +368,18 @@ def override(self, **overrides):
         """
         restore = {a: getattr(self, a) for a in overrides}
         try:
-            # Preserve order so that settings that depend on each other can be overridden together i.e., always override zarr version before sharding
+            # Preserve order so that settings that depend on each other can be overridden together i.e., always override zarr version before sharding.
+            # Otherwise an error would be raised setting sharding before zarr version if the zarr version is 2.
             for k in self._config:
                 if k in overrides:
                     setattr(self, k, overrides.get(k))
             yield None
         finally:
-            # TODO: does the order need to be preserved when restoring?
-            for attr, value in restore.items():
-                setattr(self, attr, value)
+            # In the try block, we went in the forward order i.e., zarr version before sharding, but in the reset here, we go in the reverse order i.e., sharding before zarr version.
+            # Otherwise an error would be raised if we reversed the zarr version first and it was 3 previously.
+            for k in reversed(self._config.keys()):
+                if k in restore:
+                    setattr(self, k, restore.get(k))
 
     def __repr__(self) -> str:
         params = "".join(f"\t{k}={v!r},\n" for k, v in self._config.items())

tests/test_io_elementwise.py

@@ -913,10 +913,18 @@ def test_h5_unchunked(
 
 
 @pytest.mark.zarr_io
-def test_write_auto_sharded(tmp_path: Path):
+@pytest.mark.parametrize(
+    "override",
+    [
+        {"auto_shard_zarr_v3": True, "zarr_write_format": 3},
+        {"zarr_write_format": 3, "auto_shard_zarr_v3": True},
+    ],
+    ids=["shard_first", "write_format_first"],
+)
+def test_write_auto_sharded(tmp_path: Path, override: dict):
     path = tmp_path / "check.zarr"
     adata = gen_adata((1000, 100), **GEN_ADATA_NO_XARRAY_ARGS)
-    with ad.settings.override(auto_shard_zarr_v3=True, zarr_write_format=3):
+    with ad.settings.override(**override):
         adata.write_zarr(path)
 
     check_all_sharded(zarr.open(path))