remove empty raw group when empty

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.5.3]
+
+### Fix
+- Fix bug in AnnData backend where "raw" entry with encoding-type "null" is written by default in newer anndata versions, which causes compatibility issues with older anndata versions. Now the "raw" entry is removed after writing if it has encoding-type "null".
+
 ## [0.5.2]
 
 ### Fix

src/ngio/tables/backends/_anndata.py

@@ -81,6 +81,17 @@ def _write_to_memory_store(
             suppress_warnings=True,
         )
 
+    def _cleanup_after_write(self) -> None:
+        """Clean up any temporary data after writing."""
+        group = self._group_handler._group
+        try:
+            raw_group = group["raw"]
+        except KeyError:
+            return
+        # Remove "raw" entry (encoding-type "null") that anndata <0.11 can't read
+        if dict(raw_group.attrs).get("encoding-type") == "null":
+            del group["raw"]
+
     def write_from_anndata(self, table: AnnData) -> None:
         """Serialize the table from an AnnData object."""
         # Make sure to use the correct zarr format
@@ -112,6 +123,7 @@ def write_from_anndata(self, table: AnnData) -> None:
                 "Please make sure to use a compatible "
                 "store like a LocalStore, or FsspecStore."
             )
+        self._cleanup_after_write()
 
     def write_from_pandas(self, table: DataFrame) -> None:
         """Serialize the table from a pandas DataFrame."""

tests/unit/tables/test_backends.py

@@ -185,6 +185,11 @@ def test_anndata_backend(tmp_path: Path):
     lf_data = backend.load_as_polars_lf()
     backend.write(lf_data, metadata={"test": "test"})
 
+    # Test that the "raw" entry with encoding-type "null" is
+    # removed after writing for compatibility with older anndata versions
+    with pytest.raises(KeyError):
+        backend._group_handler._group["raw"]
+
 
 @pytest.mark.parametrize(
     "index_label, index_type",