fix bugs in attributes wrtiting

Author: lorenzocerrone

pyproject.toml

@@ -155,7 +155,7 @@ minversion = "7.0"
 testpaths = ["tests"]
 filterwarnings = [
     "error",
-    "ignore::FutureWarning", # TODO remove after zarr-python v3 
+    "ignore::zarr.errors.ZarrUserWarning", # required for anndata
 ]
 addopts = [
     "-vv",

src/ngio/tables/backends/_abstract_backend.py

@@ -198,6 +198,14 @@ def write_metadata(self, metadata: dict | None = None) -> None:
         if metadata is None:
             metadata = {}
 
+        attrs = self._group_handler.reopen_group().attrs.asdict()
+        print(attrs, self._group_handler.full_url)
+        # This is required by anndata to identify the format
+        if "encoding-type" in attrs:
+            metadata["encoding-type"] = attrs["encoding-type"]
+        if "encoding-version" in attrs:
+            metadata["encoding-version"] = attrs["encoding-version"]
+
         backend_metadata = BackendMeta(
             backend=self.backend_name(),
             index_key=self.index_key,

src/ngio/tables/backends/_anndata.py

@@ -41,6 +41,7 @@ def implements_polars() -> bool:
 
     def load_as_anndata(self) -> AnnData:
         """Load the table as an AnnData object."""
+        settings.zarr_write_format = self._group_handler.zarr_format
         anndata = custom_anndata_read_zarr(self._group_handler._group)
         anndata = normalize_anndata(anndata, index_key=self.index_key)
         return anndata

src/ngio/utils/_zarr_utils.py

@@ -166,7 +166,7 @@ def __repr__(self) -> str:
     @property
     def store(self) -> Store:
         """Return the store of the group."""
-        return self.group.store
+        return self._group.store
 
     @property
     def full_url(self) -> str | None:
@@ -180,7 +180,7 @@ def full_url(self) -> str | None:
     @property
     def zarr_format(self) -> Literal[2, 3]:
         """Return the Zarr format version."""
-        return self.group.metadata.zarr_format
+        return self._group.metadata.zarr_format
 
     @property
     def mode(self) -> AccessModeLiteral:
@@ -216,22 +216,30 @@ def remove_lock(self) -> None:
 
         raise NgioValueError("The lock is still in use. Cannot remove it.")
 
+    def reopen_group(self) -> zarr.Group:
+        """Reopen the group.
+
+        This is useful when the group has been modified
+        outside of the handler.
+        """
+        if self.mode == "r":
+            mode = "r"
+        else:
+            mode = "r+"
+        return zarr.open_group(
+            store=self._group.store,
+            path=self._group.path,
+            mode=mode,
+            zarr_format=self._group.metadata.zarr_format,
+        )
+
     @property
     def group(self) -> zarr.Group:
         """Return the group."""
         if self._parallel_safe:
             # If we are parallel safe, we need to reopen the group
             # to make sure that the attributes are up to date
-            if self.mode == "r":
-                mode = "r"
-            else:
-                mode = "r+"
-            return zarr.open_group(
-                store=self._group.store,
-                path=self._group.path,
-                mode=mode,
-                zarr_format=self._group.metadata.zarr_format,
-            )
+            return self.reopen_group()
         return self._group
 
     def add_to_cache(self, key: str, value: object) -> None: