Fix read_zarr for consolidated metadata and use directly on zarr.Group

anndata/_io/zarr.py

@@ -62,7 +62,10 @@ def read_zarr(store: Union[str, Path, MutableMapping, zarr.Group]) -> AnnData:
     if isinstance(store, Path):
         store = str(store)
 
-    f = zarr.open(store, mode="r")
+    if isinstance(store, zarr.Group):
+        f = store
+    else:
+        f = zarr.open(store, mode="r")
 
     # Read with handling for backwards compat
     def callback(func, elem_name: str, elem, iospec):

anndata/tests/test_io_elementwise.py

@@ -180,3 +180,24 @@ def test_override_specification():
         )
         def _(store, key, adata):
             pass
+
+
+@pytest.mark.parametrize("consolidated", [True, False])
+def test_read_zarr_from_group(tmp_path, consolidated):
+    # https://github.com/scverse/anndata/issues/1056
+    pth = tmp_path / "test.zarr"
+    adata = gen_adata((3, 2))
+
+    with zarr.open(pth, mode="w") as z:
+        write_elem(z, "table/table", adata)
+
+        if consolidated:
+            zarr.convenience.consolidate_metadata(z.store)
+
+    if consolidated:
+        read_func = zarr.open_consolidated
+    else:
+        read_func = zarr.open
+
+    with read_func(pth) as z:
+        assert_equal(ad.read_zarr(z["table/table"]), adata)

docs/release-notes/0.9.2.md

@@ -5,3 +5,4 @@
 
 * Fix ufuncs of views like `adata.X[:10].cov(axis=0)` returning views {pr}`1043` {user}`flying-sheep`
 * Fix instantiating AnnData where `.X` is a `DataFrame` with an integer valued index  {pr}`1002` {user}`flying-sheep`
+* Fix {func}`~anndata.read_zarr` when used on `zarr.Group` {pr}`1057` {user}`ivirshup`