(feat): use numpy nan-able string type for anndata.experimental.MaskedArray

docs/release-notes/2011.feature.md

@@ -0,0 +1 @@
+Use {attr}`numpy.dtypes.StringDType` with `na_object` set to {attr}`pandas.NA` for nullable string data with {class}`anndata.experimental.backed.Dataset2D` {user}`ilan-gold`

src/anndata/_io/specs/lazy_methods.py

@@ -15,6 +15,7 @@
 from anndata._core.xarray import Dataset2D, requires_xarray
 from anndata.abc import CSCDataset, CSRDataset
 from anndata.compat import (
+    NULLABLE_NUMPY_STRING_TYPE,
     DaskArray,
     H5Array,
     H5Group,
@@ -259,8 +260,7 @@ def _gen_xarray_dict_iterator_from_elems(
                     "base_path_or_zarr_group": v.base_path_or_zarr_group,
                     "elem_name": v.elem_name,
                     "is_nullable_string": isinstance(v, MaskedArray)
-                    and v.dtype  # CategoricalArray dtype access requires a read nad is not necessary here
-                    == np.dtype("O"),
+                    and v.dtype == NULLABLE_NUMPY_STRING_TYPE,
                 },
             )
         elif k == dim_name:

src/anndata/compat/__init__.py

@@ -404,3 +404,10 @@ def _map_cat_to_str(cat: pd.Categorical) -> pd.Categorical:
         return cat.map(str, na_action="ignore")
     else:
         return cat.map(str)
+
+
+NULLABLE_NUMPY_STRING_TYPE = (
+    np.dtype("O")
+    if Version(np.__version__) < Version("2")
+    else np.dtypes.StringDType(na_object=pd.NA)
+)

src/anndata/experimental/backed/_lazy_arrays.py

@@ -3,7 +3,6 @@
 from functools import cached_property
 from typing import TYPE_CHECKING, Generic, TypeVar
 
-import numpy as np
 import pandas as pd
 
 from anndata._core.index import _subset
@@ -12,13 +11,20 @@
 from anndata.compat import H5Array, ZarrArray
 
 from ..._settings import settings
-from ...compat import XBackendArray, XDataArray, XZarrArrayWrapper
+from ...compat import (
+    NULLABLE_NUMPY_STRING_TYPE,
+    XBackendArray,
+    XDataArray,
+    XZarrArrayWrapper,
+)
 from ...compat import xarray as xr
 
 if TYPE_CHECKING:
     from pathlib import Path
     from typing import Literal
 
+    import numpy as np
+
     from anndata._core.index import Index
     from anndata.compat import ZarrGroup
 
@@ -146,7 +152,8 @@
             extension_array = pd.arrays.BooleanArray(values, mask=mask)
         elif self._dtype_str == "nullable-string-array":
             # https://github.com/pydata/xarray/issues/10419
-            values[mask] = np.nan
+            values = values.astype(self.dtype)
+            values[mask] = pd.NA
             return values
         else:
             msg = f"Invalid dtype_str {self._dtype_str}"
@@ -164,7 +171,7 @@
             return pd.BooleanDtype()
         elif self._dtype_str == "nullable-string-array":
             # https://github.com/pydata/xarray/issues/10419
-            return np.dtype("O")
+            return NULLABLE_NUMPY_STRING_TYPE
         msg = f"Invalid dtype_str {self._dtype_str}"
         raise RuntimeError(msg)