spatialdata 0.2.5__tar.gz → 0.2.6__tar.gz

{spatialdata-0.2.5 → spatialdata-0.2.6}/.github/workflows/test.yaml

@@ -18,11 +18,11 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: ["3.9", "3.12"]
+                python: ["3.10", "3.12"]
                 os: [ubuntu-latest]
                 include:
                     - os: macos-latest
-                      python: "3.9"
+                      python: "3.10"
                     - os: macos-latest
                       python: "3.12"
                       pip-flags: "--pre"

{spatialdata-0.2.5 → spatialdata-0.2.6}/.mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False

{spatialdata-0.2.5 → spatialdata-0.2.6}/.pre-commit-config.yaml

@@ -2,14 +2,14 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 ci:
     skip: []
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.8.0
+      rev: 24.10.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -17,17 +17,17 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
+      rev: 1.19.1
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.11.2
+      rev: v1.13.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.6.8
+      rev: v0.7.3
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

{spatialdata-0.2.5 → spatialdata-0.2.6}/CHANGELOG.md

@@ -8,13 +8,35 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.2.5] - 2024-06-11
+## [0.2.6] - 2024-11-26
+
+### Added
+
+-   Added `set_channel_names` method to `SpatialData` to change the channel names of an
+    image element in `SpatialData` #786
+-   Added `write_channel_names` method to `SpatialData` to overwrite channel metadata on disk
+    without overwriting the image array itself. #786
+
+### Changed
+
+-   Argument `c_coords` is moved out of kwargs for the `ImageModel`s. #779
+-   `get_channels` is marked for deprecation in `SpatialData` v0.3.0. Function is replaced
+    by `get_channel_names` #786
+-   Updated dependency of `multiscale-spatial-image` #792
+-   Adjust to new version of `xarray` with `DataTree` # 752
+
+### Fixed
+
+-   Updated deprecated default stages of `pre-commit` #771
+-   Preserve points `feature_key` during queries #794
+
+## [0.2.5] - 2024-11-06
 
 ### Fixed
 
 -   Incompatibility issues due to newest release of `multiscale-spatial-image` #760
 
-## [0.2.4] - 2024-06-11
+## [0.2.4] - 2024-11-06
 
 ### Major
 

{spatialdata-0.2.5 → spatialdata-0.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: spatialdata
-Version: 0.2.5
+Version: 0.2.6
 Summary: Spatial data format.
 Project-URL: Documentation, https://spatialdata.scverse.org/en/latest
 Project-URL: Source, https://github.com/scverse/spatialdata.git
@@ -36,15 +36,14 @@ License: BSD 3-Clause License
         CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-License-File: LICENSE
-Requires-Python: >=3.9
+Requires-Python: <3.13,>=3.10
 Requires-Dist: anndata>=0.9.1
 Requires-Dist: click
 Requires-Dist: dask-image
 Requires-Dist: dask>=2024.4.1
 Requires-Dist: fsspec<=2023.6
 Requires-Dist: geopandas>=0.14
-Requires-Dist: multiscale-spatial-image<2.0.0,>=1.0.0
+Requires-Dist: multiscale-spatial-image>=2.0.2
 Requires-Dist: networkx
 Requires-Dist: numba
 Requires-Dist: numpy
@@ -59,16 +58,16 @@ Requires-Dist: setuptools
 Requires-Dist: shapely>=2.0.1
 Requires-Dist: spatial-image>=1.1.0
 Requires-Dist: typing-extensions>=4.8.0
-Requires-Dist: xarray-datatree
 Requires-Dist: xarray-schema
 Requires-Dist: xarray-spatial>=0.3.5
-Requires-Dist: xarray<2024.10.0
-Requires-Dist: zarr
+Requires-Dist: xarray>=2024.10.0
+Requires-Dist: zarr<3
 Provides-Extra: dev
 Requires-Dist: bump2version; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: ipython>=8.6.0; extra == 'docs'
 Requires-Dist: myst-nb; extra == 'docs'
+Requires-Dist: sphinx-autobuild; extra == 'docs'
 Requires-Dist: sphinx-autodoc-typehints; extra == 'docs'
 Requires-Dist: sphinx-book-theme>=1.0.0; extra == 'docs'
 Requires-Dist: sphinx-copybutton; extra == 'docs'

{spatialdata-0.2.5 → spatialdata-0.2.6}/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.5'
-__version_tuple__ = version_tuple = (0, 2, 5)
+__version__ = version = '0.2.6'
+__version_tuple__ = version_tuple = (0, 2, 6)

{spatialdata-0.2.5 → spatialdata-0.2.6}/pyproject.toml

@@ -15,7 +15,7 @@ maintainers = [
 urls.Documentation = "https://spatialdata.scverse.org/en/latest"
 urls.Source = "https://github.com/scverse/spatialdata.git"
 urls.Home-page = "https://github.com/scverse/spatialdata.git"
-requires-python = ">=3.9"
+requires-python = ">=3.10, <3.13" # include 3.13 once multiscale-spatial-image conflicts are resolved
 dynamic= [
   "version" # allow version to be set by git tags
 ]
@@ -28,7 +28,7 @@ dependencies = [
     "dask>=2024.4.1",
     "fsspec<=2023.6",
     "geopandas>=0.14",
-    "multiscale_spatial_image>=1.0.0,<2.0.0",
+    "multiscale_spatial_image>=2.0.2",
     "networkx",
     "numba",
     "numpy",
@@ -43,11 +43,10 @@ dependencies = [
     "scikit-image",
     "scipy",
     "typing_extensions>=4.8.0",
-    "xarray<2024.10.0",
-    "xarray-datatree",
+    "xarray>=2024.10.0",
     "xarray-schema",
     "xarray-spatial>=0.3.5",
-    "zarr",
+    "zarr<3",
 ]
 
 [project.optional-dependencies]
@@ -56,6 +55,7 @@ dev = [
 ]
 docs = [
     "sphinx>=4.5",
+	"sphinx-autobuild",
     "sphinx-book-theme>=1.0.0",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
@@ -102,7 +102,7 @@ filterwarnings = [
 
 [tool.black]
 line-length = 120
-target-version = ['py39']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 (
@@ -147,7 +147,7 @@ exclude = [
     "setup.py",
 ]
 line-length = 120
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 ignore = [

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/_deepcopy.py

@@ -7,9 +7,8 @@ from anndata import AnnData
 from dask.array.core import Array as DaskArray
 from dask.array.core import from_array
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata.models._utils import SpatialElement

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/centroids.py

@@ -7,10 +7,9 @@ import dask.array as da
 import pandas as pd
 import xarray as xr
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import MultiPolygon, Point, Polygon
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata._core.operations.transform import transform
 from spatialdata.models import get_axes_names
@@ -86,7 +85,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
             centroids[label_value] += count * i.values.item()
 
     all_labels_values, all_labels_counts = da.unique(xdata.data, return_counts=True)
-    all_labels = dict(zip(all_labels_values.compute(), all_labels_counts.compute()))
+    all_labels = dict(zip(all_labels_values.compute(), all_labels_counts.compute(), strict=True))
     for label_value in centroids:
         centroids[label_value] /= all_labels[label_value]
     centroids = dict(sorted(centroids.items(), key=lambda x: x[0]))
@@ -132,7 +131,7 @@ def _(e: GeoDataFrame, coordinate_system: str = "global") -> DaskDataFrame:
     if isinstance(first_geometry, Point):
         xy = e.geometry.get_coordinates().values
     else:
-        assert isinstance(first_geometry, (Polygon, MultiPolygon)), (
+        assert isinstance(first_geometry, Polygon | MultiPolygon), (
             f"Expected a GeoDataFrame either composed entirely of circles (Points with the `radius` column) or"
             f" Polygons/MultiPolygons. Found {type(first_geometry)} instead."
         )

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/concatenate.py

@@ -51,7 +51,7 @@ def _concatenate_tables(
             raise ValueError("`instance_key` must be specified if tables have different instance keys")
 
     tables_l = []
-    for table_region_key, table_instance_key, table in zip(region_keys, instance_keys, tables):
+    for table_region_key, table_instance_key, table in zip(region_keys, instance_keys, tables, strict=True):
         rename_dict = {}
         if table_region_key != region_key:
             rename_dict[table_region_key] = region_key
@@ -239,7 +239,7 @@ def _fix_ensure_unique_element_names(
             tables[new_name] = table
         tables_by_sdata.append(tables)
     sdatas_fixed = []
-    for elements, tables in zip(elements_by_sdata, tables_by_sdata):
+    for elements, tables in zip(elements_by_sdata, tables_by_sdata, strict=True):
         sdata = SpatialData.init_from_elements(elements, tables=tables)
         sdatas_fixed.append(sdata)
     return sdatas_fixed

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/data_extent.py

@@ -8,10 +8,9 @@ from typing import Union
 import numpy as np
 import pandas as pd
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import MultiPolygon, Point, Polygon
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata._core.operations.transform import transform
 from spatialdata._core.spatialdata import SpatialData
@@ -71,7 +70,7 @@ def _get_extent_of_polygons_multipolygons(
     -------
     The bounding box description.
     """
-    assert isinstance(shapes.geometry.iloc[0], (Polygon, MultiPolygon))
+    assert isinstance(shapes.geometry.iloc[0], Polygon | MultiPolygon)
     axes = get_axes_names(shapes)
     bounds = shapes["geometry"].bounds
     return {ax: (bounds[f"min{ax}"].min(), bounds[f"max{ax}"].max()) for ax in axes}
@@ -201,7 +200,7 @@ def _(
     new_max_coordinates_dict: dict[str, list[float]] = defaultdict(list)
     mask = [has_images, has_labels, has_points, has_shapes]
     include_spatial_elements = ["images", "labels", "points", "shapes"]
-    include_spatial_elements = [i for (i, v) in zip(include_spatial_elements, mask) if v]
+    include_spatial_elements = [i for (i, v) in zip(include_spatial_elements, mask, strict=True) if v]
 
     if elements is None:  # to shut up ruff
         elements = []
@@ -217,7 +216,7 @@ def _(
             assert isinstance(transformations, dict)
             coordinate_systems = list(transformations.keys())
             if coordinate_system in coordinate_systems:
-                if isinstance(element_obj, (DaskDataFrame, GeoDataFrame)):
+                if isinstance(element_obj, DaskDataFrame | GeoDataFrame):
                     extent = get_extent(element_obj, coordinate_system=coordinate_system, exact=exact)
                 else:
                     extent = get_extent(element_obj, coordinate_system=coordinate_system)
@@ -254,7 +253,7 @@ def _get_extent_of_shapes(e: GeoDataFrame) -> BoundingBoxDescription:
     first_geometry = e_temp["geometry"].iloc[0]
     if isinstance(first_geometry, Point):
         return _get_extent_of_circles(e)
-    assert isinstance(first_geometry, (Polygon, MultiPolygon))
+    assert isinstance(first_geometry, Polygon | MultiPolygon)
     return _get_extent_of_polygons_multipolygons(e)
 
 

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/_utils.py

@@ -2,8 +2,7 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
-from datatree import DataTree
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata.models import SpatialElement
 
@@ -115,7 +114,7 @@ def transform_to_data_extent(
     }
 
     for _, element_name, element in sdata_raster.gen_spatial_elements():
-        if isinstance(element, (DataArray, DataTree)):
+        if isinstance(element, DataArray | DataTree):
             rasterized = rasterize(
                 element,
                 axes=data_extent_axes,

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/aggregate.py

@@ -10,11 +10,10 @@ import geopandas as gpd
 import numpy as np
 import pandas as pd
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from scipy import sparse
 from shapely import Point
-from xarray import DataArray
+from xarray import DataArray, DataTree
 from xrspatial import zonal_stats
 
 from spatialdata._core.operations._utils import _parse_element
@@ -246,7 +245,7 @@ def _create_sdata_from_table_and_shapes(
     table = TableModel.parse(table, region=shapes_name, region_key=region_key, instance_key=instance_key)
 
     # labels case, needs conversion from str to int
-    if isinstance(shapes, (DataArray, DataTree)):
+    if isinstance(shapes, DataArray | DataTree):
         table.obs[instance_key] = table.obs[instance_key].astype(int)
 
     if deepcopy:

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/map.py

@@ -1,15 +1,14 @@
 from __future__ import annotations
 
-from collections.abc import Iterable, Mapping
+from collections.abc import Callable, Iterable, Mapping
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any
 
 import dask.array as da
 from dask.array.overlap import coerce_depth
-from datatree import DataTree
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
-from spatialdata.models._utils import get_axes_names, get_channels, get_raster_model_from_data_dims
+from spatialdata.models._utils import get_axes_names, get_channel_names, get_raster_model_from_data_dims
 from spatialdata.transformations import get_transformation
 
 __all__ = ["map_raster"]
@@ -122,7 +121,7 @@ def map_raster(
 
     if "c" in dims:
         if c_coords is None:
-            c_coords = range(arr.shape[0]) if arr.shape[0] != len(get_channels(data)) else get_channels(data)
+            c_coords = range(arr.shape[0]) if arr.shape[0] != len(get_channel_names(data)) else get_channel_names(data)
     else:
         c_coords = None
     if transformations is None:

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/rasterize.py

@@ -5,10 +5,9 @@ import datashader as ds
 import numpy as np
 from dask.array import Array as DaskArray
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import Point
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata._core.operations._utils import _parse_element
 from spatialdata._core.operations.transform import transform

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/rasterize_bins.py

@@ -73,7 +73,7 @@ def rasterize_bins(
     """
     element = sdata[bins]
     table = sdata.tables[table_name]
-    if not isinstance(element, (GeoDataFrame, DaskDataFrame)):
+    if not isinstance(element, GeoDataFrame | DaskDataFrame):
         raise ValueError("The bins should be a GeoDataFrame or a DaskDataFrame.")
 
     _, region_key, instance_key = get_table_keys(table)
@@ -94,7 +94,7 @@ def rasterize_bins(
     keys = ([value_key] if isinstance(value_key, str) else value_key) if value_key is not None else table.var_names
 
     if (value_key is None or any(key in table.var_names for key in keys)) and not isinstance(
-        table.X, (csc_matrix, np.ndarray)
+        table.X, csc_matrix | np.ndarray
     ):
         raise ValueError(
             "To speed up bins rasterization, the X matrix in the table, when sparse, should be a csc_matrix matrix. "
@@ -162,7 +162,7 @@ def rasterize_bins(
             sub_x = sub_df.geometry.x.values
             sub_y = sub_df.geometry.y.values
         else:
-            assert isinstance(sub_df.iloc[0].geometry, (Polygon, MultiPolygon))
+            assert isinstance(sub_df.iloc[0].geometry, Polygon | MultiPolygon)
             sub_x = sub_df.centroid.x
             sub_y = sub_df.centroid.y
     else:

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/transform.py

@@ -10,15 +10,14 @@ import dask_image.ndinterp
 import numpy as np
 from dask.array.core import Array as DaskArray
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import Point
-from xarray import DataArray
+from xarray import DataArray, Dataset, DataTree
 
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
 from spatialdata.models import SpatialElement, get_axes_names, get_model
-from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM, get_channels
+from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM, get_channel_names
 from spatialdata.transformations._utils import _get_scale, compute_coordinates, scale_radii
 
 if TYPE_CHECKING:
@@ -161,13 +160,13 @@ def _set_transformation_for_transformed_elements(
         assert to_coordinate_system is None
 
     to_prepend: BaseTransformation | None
-    if isinstance(element, (DataArray, DataTree)):
+    if isinstance(element, DataArray | DataTree):
         if maintain_positioning:
             assert raster_translation is not None
             to_prepend = Sequence([raster_translation, transformation.inverse()])
         else:
             to_prepend = raster_translation
-    elif isinstance(element, (GeoDataFrame, DaskDataFrame)):
+    elif isinstance(element, GeoDataFrame | DaskDataFrame):
         assert raster_translation is None
         to_prepend = transformation.inverse() if maintain_positioning else Identity()
     else:
@@ -368,7 +367,7 @@ def _(
         channel_names = None
     elif schema in (Image2DModel, Image3DModel):
         kwargs = {}
-        channel_names = get_channels(data)
+        channel_names = get_channel_names(data)
     else:
         raise ValueError(f"DataTree with schema {schema} not supported")
 
@@ -393,8 +392,11 @@ def _(
             raster_translation = raster_translation_single_scale
         # we set a dummy empty dict for the transformation that will be replaced with the correct transformation for
         # each scale later in this function, when calling set_transformation()
-        transformed_dict[k] = DataArray(transformed_dask, dims=xdata.dims, name=xdata.name, attrs={TRANSFORM_KEY: {}})
+        transformed_dict[k] = Dataset(
+            {"image": DataArray(transformed_dask, dims=xdata.dims, name=xdata.name, attrs={TRANSFORM_KEY: {}})}
+        )
         if channel_names is not None:
+            # This expression returns a dataset now.
             transformed_dict[k] = transformed_dict[k].assign_coords(c=channel_names)
 
     # mypy thinks that schema could be ShapesModel, PointsModel, ...

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/operations/vectorize.py

@@ -9,11 +9,10 @@ import pandas as pd
 import shapely
 import skimage.measure
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import MultiPolygon, Point, Polygon
 from skimage.measure._regionprops import RegionProperties
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata._core.centroids import get_centroids
 from spatialdata._core.operations.aggregate import aggregate
@@ -106,7 +105,7 @@ def _(element: DataArray | DataTree, **kwargs: Any) -> GeoDataFrame:
 @to_circles.register(GeoDataFrame)
 def _(element: GeoDataFrame, **kwargs: Any) -> GeoDataFrame:
     assert len(kwargs) == 0
-    if isinstance(element.geometry.iloc[0], (Polygon, MultiPolygon)):
+    if isinstance(element.geometry.iloc[0], Polygon | MultiPolygon):
         radius = np.sqrt(element.geometry.area / np.pi)
         centroids = _get_centroids(element)
         obs = pd.DataFrame({"radius": radius})
@@ -258,7 +257,7 @@ def _dissolve_on_overlaps(label: int, group: GeoDataFrame) -> GeoDataFrame:
 
 @to_polygons.register(GeoDataFrame)
 def _(gdf: GeoDataFrame, buffer_resolution: int = 16) -> GeoDataFrame:
-    if isinstance(gdf.geometry.iloc[0], (Polygon, MultiPolygon)):
+    if isinstance(gdf.geometry.iloc[0], Polygon | MultiPolygon):
         return gdf
     if isinstance(gdf.geometry.iloc[0], Point):
         ShapesModel.validate_shapes_not_mixed_types(gdf)
@@ -274,7 +273,7 @@ def _(gdf: GeoDataFrame, buffer_resolution: int = 16) -> GeoDataFrame:
             # TODO replace with a function to copy the metadata (the parser could also do this): https://github.com/scverse/spatialdata/issues/258
             buffered_df.attrs[ShapesModel.TRANSFORM_KEY] = gdf.attrs[ShapesModel.TRANSFORM_KEY]
             return buffered_df
-        assert isinstance(gdf.geometry.iloc[0], (Polygon, MultiPolygon))
+        assert isinstance(gdf.geometry.iloc[0], Polygon | MultiPolygon)
         return gdf
     raise RuntimeError("Unsupported geometry type: " f"{type(gdf.geometry.iloc[0])}")
 

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/query/_utils.py

@@ -5,8 +5,7 @@ from typing import Any
 import numba as nb
 import numpy as np
 from anndata import AnnData
-from datatree import DataTree
-from xarray import DataArray
+from xarray import DataArray, Dataset, DataTree
 
 from spatialdata._core._elements import Tables
 from spatialdata._core.spatialdata import SpatialData
@@ -96,7 +95,7 @@ def get_bounding_box_corners(
     return output.squeeze().drop_vars("box")
 
 
-@nb.njit(parallel=False, nopython=True)
+@nb.jit(parallel=False, nopython=True)
 def _create_slices_and_translation(
     min_values: nb.types.Array,
     max_values: nb.types.Array,
@@ -138,7 +137,7 @@ def _process_data_tree_query_result(query_result: DataTree) -> DataTree | None:
     if len(scales_to_keep) == 0:
         return None
 
-    d = {k: d[k] for k in scales_to_keep}
+    d = {k: Dataset({"image": d[k]}) for k in scales_to_keep}
     result = DataTree.from_dict(d)
 
     # Rechunk the data to avoid irregular chunks

{spatialdata-0.2.5 → spatialdata-0.2.6}/src/spatialdata/_core/query/relational_query.py

@@ -13,9 +13,8 @@ import numpy as np
 import pandas as pd
 from anndata import AnnData
 from dask.dataframe import DataFrame as DaskDataFrame
-from datatree import DataTree
 from geopandas import GeoDataFrame
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
@@ -653,7 +652,7 @@ def join_spatialelement_table(
     if sdata is not None:
         elements_dict = _create_sdata_elements_dict_for_join(sdata, spatial_element_names)
     else:
-        derived_sdata = SpatialData.from_elements_dict(dict(zip(spatial_element_names, spatial_elements)))
+        derived_sdata = SpatialData.from_elements_dict(dict(zip(spatial_element_names, spatial_elements, strict=True)))
         element_types = ["labels", "shapes", "points"]
         elements_dict = defaultdict(lambda: defaultdict(dict))
         for element_type in element_types:
@@ -919,7 +918,7 @@ def get_values(
             x = matched_table[:, value_key_values].X
             import scipy
 
-            if isinstance(x, (scipy.sparse.csr_matrix, scipy.sparse.csc_matrix, scipy.sparse.coo_matrix)):
+            if isinstance(x, scipy.sparse.csr_matrix | scipy.sparse.csc_matrix | scipy.sparse.coo_matrix):
                 x = x.todense()
             df = pd.DataFrame(x, columns=value_key_values)
         if origin == "obsm":