Remove xarray-schema; validate() are now class methods (#1066)

* remove xarray-schema; validate() are now class methods

* small code cleanup

* remove unused model instances; fix validation for table (should not modify the object)

* fix test_set_table_annotates_spatialelement

* remove deprecation warning for raster and table model __init__

Author: LucaMarconato

pyproject.toml

@@ -48,7 +48,6 @@ dependencies = [
     "typing_extensions>=4.8.0",
     "universal_pathlib>=0.2.6",
     "xarray>=2024.10.0",
-    "xarray-schema",
     "xarray-spatial>=0.3.5",
     "zarr>=3.0.0",
 ]

src/spatialdata/_core/_deepcopy.py

@@ -79,7 +79,7 @@ def _(element: DataTree) -> DataTree:
         msi[key][variable].data = from_array(msi[key][variable].data)
         element[key][variable].data = from_array(element[key][variable].data)
     assert model in [Image2DModel, Image3DModel, Labels2DModel, Labels3DModel]
-    model().validate(msi)
+    model.validate(msi)
     return msi
 
 

src/spatialdata/_core/_elements.py

@@ -72,10 +72,10 @@ def __setitem__(self, key: str, value: Raster_T) -> None:
             raise TypeError(f"Unknown element type with schema: {schema!r}.")
         ndim = len(get_axes_names(value))
         if ndim == 3:
-            Image2DModel().validate(value)
+            Image2DModel.validate(value)
             super().__setitem__(key, value)
         elif ndim == 4:
-            Image3DModel().validate(value)
+            Image3DModel.validate(value)
             super().__setitem__(key, value)
         else:
             NotImplementedError("TODO: implement for ndim > 4.")
@@ -89,10 +89,10 @@ def __setitem__(self, key: str, value: Raster_T) -> None:
             raise TypeError(f"Unknown element type with schema: {schema!r}.")
         ndim = len(get_axes_names(value))
         if ndim == 2:
-            Labels2DModel().validate(value)
+            Labels2DModel.validate(value)
             super().__setitem__(key, value)
         elif ndim == 3:
-            Labels3DModel().validate(value)
+            Labels3DModel.validate(value)
             super().__setitem__(key, value)
         else:
             NotImplementedError("TODO: implement for ndim > 3.")
@@ -104,7 +104,7 @@ def __setitem__(self, key: str, value: GeoDataFrame) -> None:
         schema = get_model(value)
         if schema != ShapesModel:
             raise TypeError(f"Unknown element type with schema: {schema!r}.")
-        ShapesModel().validate(value)
+        ShapesModel.validate(value)
         super().__setitem__(key, value)
 
 
@@ -114,7 +114,7 @@ def __setitem__(self, key: str, value: DaskDataFrame) -> None:
         schema = get_model(value)
         if schema != PointsModel:
             raise TypeError(f"Unknown element type with schema: {schema!r}.")
-        PointsModel().validate(value)
+        PointsModel.validate(value)
         super().__setitem__(key, value)
 
 
@@ -124,5 +124,5 @@ def __setitem__(self, key: str, value: AnnData) -> None:
         schema = get_model(value)
         if schema != TableModel:
             raise TypeError(f"Unknown element type with schema: {schema!r}.")
-        TableModel().validate(value)
+        TableModel.validate(value)
         super().__setitem__(key, value)

src/spatialdata/_core/operations/rasterize.py

@@ -602,7 +602,7 @@ def rasterize_images_labels(
     set_transformation(transformed_data, sequence, target_coordinate_system)
 
     transformed_data = compute_coordinates(transformed_data)
-    schema().validate(transformed_data)
+    schema.validate(transformed_data)
     return transformed_data
 
 

src/spatialdata/_core/operations/transform.py

@@ -333,7 +333,7 @@ def _(
         to_coordinate_system=to_coordinate_system,
     )
     transformed_data = compute_coordinates(transformed_data)
-    schema().validate(transformed_data)
+    schema.validate(transformed_data)
     return transformed_data
 
 
@@ -419,7 +419,7 @@ def _(
         to_coordinate_system=to_coordinate_system,
     )
     transformed_data = compute_coordinates(transformed_data)
-    schema().validate(transformed_data)
+    schema.validate(transformed_data)
     return transformed_data
 
 

src/spatialdata/_core/spatialdata.py

@@ -57,15 +57,6 @@
         SpatialDataFormatType,
     )
 
-# schema for elements
-Label2D_s = Labels2DModel()
-Label3D_s = Labels3DModel()
-Image2D_s = Image2DModel()
-Image3D_s = Image3DModel()
-Shape_s = ShapesModel()
-Point_s = PointsModel()
-Table_s = TableModel()
-
 
 class SpatialData:
     """
@@ -199,7 +190,7 @@ def validate_table_in_spatialdata(self, table: AnnData) -> None:
         UserWarning
             The dtypes of the instance key column in the table and the annotation target do not match.
         """
-        TableModel().validate(table)
+        TableModel.validate(table)
         if TableModel.ATTRS_KEY in table.uns:
             region, _, instance_key = get_table_keys(table)
             region = region if isinstance(region, list) else [region]
@@ -349,8 +340,13 @@ def _set_table_annotation_target(
         ValueError
             If `instance_key` is not present in the `table.obs` columns.
         """
-        TableModel()._validate_set_region_key(table, region_key)
-        TableModel()._validate_set_instance_key(table, instance_key)
+        old_attrs = table.uns.get(TableModel.ATTRS_KEY)
+        # _validate_set_region_key and _validate_set_instance_key will raise an error if table.uns[ATTRS_KEY] is None,
+        # so let's initialize it here. Below it will be replaced with the actual metadata.
+        if old_attrs is None:
+            table.uns[TableModel.ATTRS_KEY] = {}
+        TableModel._validate_set_region_key(table, region_key)
+        TableModel._validate_set_instance_key(table, instance_key)
         attrs = {
             TableModel.REGION_KEY: region,
             TableModel.REGION_KEY_KEY: region_key,
@@ -393,8 +389,8 @@ def _change_table_annotation_target(
         attrs = table.uns[TableModel.ATTRS_KEY]
         table_region_key = region_key if region_key else attrs.get(TableModel.REGION_KEY_KEY)
 
-        TableModel()._validate_set_region_key(table, region_key)
-        TableModel()._validate_set_instance_key(table, instance_key)
+        TableModel._validate_set_region_key(table, region_key)
+        TableModel._validate_set_instance_key(table, instance_key)
         check_target_region_column_symmetry(table, table_region_key, region)
         attrs[TableModel.REGION_KEY] = region
 
@@ -1822,7 +1818,7 @@ def tables(self, tables: dict[str, AnnData]) -> None:
         self._shared_keys = self._shared_keys - set(self._tables.keys())
         self._tables = Tables(shared_keys=self._shared_keys)
         for k, v in tables.items():
-            TableModel().validate(v)
+            TableModel.validate(v)
             self._tables[k] = v
 
     @staticmethod

src/spatialdata/_io/io_table.py

@@ -56,7 +56,7 @@ def write_table(
 ) -> None:
     if TableModel.ATTRS_KEY in table.uns:
         region, region_key, instance_key = get_table_keys(table)
-        TableModel().validate(table)
+        TableModel.validate(table)
     else:
         region, region_key, instance_key = (None, None, None)
 

src/spatialdata/_utils.py

@@ -308,7 +308,7 @@ def _error_message_add_element() -> None:
 
 
 def _check_match_length_channels_c_dim(
-    data: DaskArray | DataArray | DataTree, c_coords: str | list[str], dims: tuple[str]
+    data: DaskArray | DataArray | DataTree, c_coords: str | list[str], dims: tuple[str, ...]
 ) -> list[str]:
     """
     Check whether channel names `c_coords` are of equal length to the `c` dimension of the data.

src/spatialdata/models/_utils.py

@@ -401,7 +401,7 @@ def set_channel_names(element: DataArray | DataTree, channel_names: str | list[s
 
     # get_model cannot be used due to circular import so get_axes_names is used instead
     if model in [Image2DModel, Image3DModel]:
-        channel_names = _check_match_length_channels_c_dim(element, channel_names, model.dims.dims)  # type: ignore[union-attr]
+        channel_names = _check_match_length_channels_c_dim(element, channel_names, model.dims)  # type: ignore[union-attr]
         if isinstance(element, DataArray):
             element = element.assign_coords(c=channel_names)
         else: