Iss1152

pyproject.toml

@@ -64,6 +64,8 @@ extra  = [
 [dependency-groups]
 dev = [
     "bump2version",
+    "prek>=0.4.11",
+    "ruff>=0.16.0",
 ]
 test = [
     "pytest",
@@ -244,3 +246,27 @@ memray-flame = "memray flamegraph --temporal"
 
 [tool.pixi.environments]
 profiling = { features = ["profiling"], solve-group = "default" }
+
+[tool.hatch.envs.test]
+dependency-groups = ["test"]
+
+[tool.hatch.envs.test-anndata-pandas]
+template = "test"
+extra-dependencies = ["zarr>=3"]
+scripts.test = ["pip list|grep anndata && pip list|grep pandas && pytest {args}"]
+scripts.test-readwrite = ["pip list|grep anndata && pip list|grep pandas && pytest tests/io/test_readwrite.py"]
+scripts.test-all = ["pip list|grep anndata && pip list|grep pandas && pytest ."]
+
+[[tool.hatch.envs.test-anndata-pandas.matrix]]
+anndata-pandas = ["0.13-2", "0.13-3", "0.12-2"]
+
+[tool.hatch.envs.test-anndata-pandas.overrides]
+matrix.anndata-pandas.extra-dependencies = [
+    # every option where the if-condition is True gets included
+    {value="anndata~=0.13", if = ["0.13-2"]},
+    {value="pandas>=2.3,<3", if = ["0.13-2"]},
+    {value="anndata~=0.13", if = ["0.13-3"]},
+    {value="pandas~=3.0", if = ["0.13-3"]},
+    {value="anndata>=0.12,<0.13", if = ["0.12-2"]},
+    {value="pandas>=2.3,<3", if = ["0.12-2"]},
+]

src/spatialdata/_io/exceptions.py

@@ -0,0 +1,26 @@
+from __future__ import annotations
+
+from ome_zarr.format import Format
+
+
+class FormatVersionUnknownError(ValueError):
+    """Exception raised when an unknown element format is encountered."""
+
+    def __init__(self, element_type: str, version_encountered: Format):
+        self.element_type = element_type
+        self.version_encountered = version_encountered
+        self.message = (
+            f"Encountered unknown element format version "
+            f"`{self.version_encountered}` for element of type `{self.element_type}`"
+        )
+        super().__init__(self.message)
+
+
+class WritingToZarrV2DeprecationWarning(DeprecationWarning):
+    """Warning raised when writing to zarr v2 format."""
+
+    message = (
+        "Writing to zarr v2 format is currently deprecated in spatialdata "
+        "and will be removed in a future version. "
+        "Please consider writing to zarr v3."
+    )

src/spatialdata/_io/io_points.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from pathlib import Path
 
 import zarr
@@ -12,6 +13,7 @@
     _write_metadata,
     overwrite_coordinate_transformations_non_raster,
 )
+from spatialdata._io.exceptions import WritingToZarrV2DeprecationWarning
 from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
 from spatialdata.models import get_axes_names
 from spatialdata.transformations._utils import (
@@ -65,6 +67,10 @@ def write_points(
     element_format
         The format of the points element used to store it.
     """
+    if element_format.zarr_format == 2:
+        warnings.warn(
+            message=WritingToZarrV2DeprecationWarning.message, category=WritingToZarrV2DeprecationWarning, stacklevel=2
+        )
     axes = get_axes_names(points)
     transformations = _get_transformations(points)
     assert transformations is not None  # mypy: validate_element() in _write_element guarantees this

src/spatialdata/_io/io_raster.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from collections.abc import Sequence
 from pathlib import Path
 from typing import Any, Literal, TypeGuard, cast
@@ -23,6 +24,7 @@
     overwrite_channel_names,
     overwrite_coordinate_transformations_raster,
 )
+from spatialdata._io.exceptions import WritingToZarrV2DeprecationWarning
 from spatialdata._io.format import (
     CurrentRasterFormat,
     RasterFormatType,
@@ -581,6 +583,11 @@ def write_image(
     raster_compressor: dict[Literal["lz4", "zstd"], int] | None = None,
     **metadata: str | JSONDict | list[JSONDict],
 ) -> None:
+    if element_format.zarr_format == 2:
+        warnings.warn(
+            message=WritingToZarrV2DeprecationWarning.message, category=WritingToZarrV2DeprecationWarning, stacklevel=2
+        )
+
     _write_raster(
         raster_type="image",
         raster_data=image,
@@ -603,6 +610,11 @@ def write_labels(
     raster_compressor: dict[Literal["lz4", "zstd"], int] | None = None,
     **metadata: JSONDict,
 ) -> None:
+    if element_format.zarr_format == 2:
+        warnings.warn(
+            message=WritingToZarrV2DeprecationWarning.message, category=WritingToZarrV2DeprecationWarning, stacklevel=2
+        )
+
     _write_raster(
         raster_type="labels",
         raster_data=labels,

src/spatialdata/_io/io_shapes.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from pathlib import Path
 from typing import Any, Literal
 
@@ -15,6 +16,7 @@
     _write_metadata,
     overwrite_coordinate_transformations_non_raster,
 )
+from spatialdata._io.exceptions import WritingToZarrV2DeprecationWarning
 from spatialdata._io.format import (
     CurrentShapesFormat,
     ShapesFormats,
@@ -93,6 +95,11 @@ def write_shapes(
         Whether to use the WKB or geoarrow encoding for GeoParquet. See :meth:`geopandas.GeoDataFrame.to_parquet` for
         details. If None, uses the value from :attr:`spatialdata.settings.shapes_geometry_encoding`.
     """
+    if element_format.zarr_format == 2:
+        warnings.warn(
+            message=WritingToZarrV2DeprecationWarning.message, category=WritingToZarrV2DeprecationWarning, stacklevel=2
+        )
+
     from spatialdata.config import settings
 
     if geometry_encoding is None:

src/spatialdata/_io/io_table.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+import warnings
+from importlib.metadata import version
 from pathlib import Path
 
 import numpy as np
@@ -9,6 +11,8 @@
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
 
+from spatialdata._io._utils import _resolve_zarr_store
+from spatialdata._io.exceptions import FormatVersionUnknownError, WritingToZarrV2DeprecationWarning
 from spatialdata._io.format import (
     CurrentTablesFormat,
     TablesFormats,
@@ -56,16 +60,43 @@ def write_table(
     group_type: str = "ngff:regions_table",
     element_format: Format = CurrentTablesFormat(),
 ) -> None:
+    if element_format.zarr_format == 2:
+        warnings.warn(
+            message=WritingToZarrV2DeprecationWarning.message, category=WritingToZarrV2DeprecationWarning, stacklevel=2
+        )
+
     if TableModel.ATTRS_KEY in table.uns:
         region, region_key, instance_key = get_table_keys(table)
         TableModel.validate(table)
     else:
         region, region_key, instance_key = (None, None, None)
 
-    write_adata(group, name, table)
-    tables_group = group[name]
-    tables_group.attrs["spatialdata-encoding-type"] = group_type
-    tables_group.attrs["region"] = region
-    tables_group.attrs["region_key"] = region_key
-    tables_group.attrs["instance_key"] = instance_key
-    tables_group.attrs["version"] = element_format.spatialdata_format_version
+    # Ensure the table group exists
+    table_group = group.require_group(name=name)
+
+    assert element_format in TablesFormats.values(), FormatVersionUnknownError(
+        element_type="table", version_encountered=element_format
+    )
+
+    if element_format.zarr_format == 3 and version("anndata") >= "0.13":
+        # `write_zarr` in anndata v0.13 and above can only write to zarr v3
+        # solution of passing resolved store directly roughly based on:
+        # https://github.com/scverse/anndata/issues/1548#issuecomment-2199801855
+
+        # resolve the store from the group
+        resolved_store = _resolve_zarr_store(table_group)
+
+        # Write the table to the path of the table group
+        table.write_zarr(store=resolved_store, consolidate_metadata=False)
+
+        table_group = group[name]
+    else:
+        table.strings_to_categoricals()
+        write_adata(group, name, table)
+        table_group = group[name]
+
+    table_group.attrs["spatialdata-encoding-type"] = group_type
+    table_group.attrs["region"] = region
+    table_group.attrs["region_key"] = region_key
+    table_group.attrs["instance_key"] = instance_key
+    table_group.attrs["version"] = element_format.spatialdata_format_version

tests/io/test_readwrite.py

@@ -16,7 +16,6 @@
 import zarr
 from anndata import AnnData
 from numpy.random import default_rng
-from packaging.version import Version
 from shapely import MultiPolygon, Polygon
 from upath import UPath
 from xarray import DataArray
@@ -1294,8 +1293,7 @@ def test_sdata_with_nan_in_obs(tmp_path: Path) -> None:
 
     Regression test for https://github.com/scverse/spatialdata/issues/399
     Previously this raised TypeError: expected unicode string, found nan.
-    Now the write succeeds, though NaN values in object-dtype columns are
-    converted to the string "nan" after round-trip.
+    Now the write succeeds, and NaN values are preserved round trip
     """
     from spatialdata.models import TableModel
 
@@ -1329,8 +1327,5 @@ def test_sdata_with_nan_in_obs(tmp_path: Path) -> None:
 
     assert r1.iloc[0] == "string"
     assert r2.iloc[1] == 3
-    if Version(pd.__version__) >= Version("3"):
-        assert pd.isna(r1.iloc[1])
-    else:  # After round-trip, NaN in object-dtype column becomes string "nan" on pandas 2
-        assert r1.iloc[1] == "nan"
+    assert pd.isna(r1.iloc[1])
     assert np.isnan(r2.iloc[0])