Merge branch 'main' into sdata_attrs

.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"

.mypy.ini

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

.pre-commit-config.yaml

@@ -2,32 +2,32 @@ 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
       rev: v4.0.0-alpha.8
       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]

CHANGELOG.md

@@ -8,12 +8,28 @@ 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
 
-## [0.2.4] - xxxx-xx-xx
+## [0.2.6] - TBD
+
+### Fixed
+
+-   Updated deprecated default stages of `pre-commit` #771
+
+## [0.2.5] - 2024-06-11
+
+### Fixed
+
+-   Incompatibility issues due to newest release of `multiscale-spatial-image` #760
+
+## [0.2.4] - 2024-06-11
+
+### Major
+
+-   Enable vectorization of `bounding_box_query` for all `SpatialData` elements. #699
 
 ### Minor
 
--   Added `shortest_path` parameter to `get_transformation_between_coordinate_systems`
--   Added `get_pyramid_levels()` utils API
+-   Added `shortest_path` parameter to `get_transformation_between_coordinate_systems` #714
+-   Added `get_pyramid_levels()` utils API #719
 -   Improved ergonomics of `concatenate()` when element names are non-unique #720
 -   Improved performance of writing images with multiscales #577
 

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
 ]
@@ -28,8 +28,9 @@ dependencies = [
     "dask>=2024.4.1",
     "fsspec<=2023.6",
     "geopandas>=0.14",
-    "multiscale_spatial_image>=1.0.0",
+    "multiscale_spatial_image>=2.0.1",
     "networkx",
+    "numba",
     "numpy",
     "ome_zarr>=0.8.4",
     "pandas",
@@ -42,8 +43,7 @@ dependencies = [
     "scikit-image",
     "scipy",
     "typing_extensions>=4.8.0",
-    "xarray",
-    "xarray-datatree",
+    "xarray>=2024.10.0",
     "xarray-schema",
     "xarray-spatial>=0.3.5",
     "zarr",
@@ -69,6 +69,7 @@ test = [
     "pytest",
     "pytest-cov",
     "pytest-mock",
+    "torch",
 ]
 torch = [
     "torch"
@@ -100,7 +101,7 @@ filterwarnings = [
 
 [tool.black]
 line-length = 120
-target-version = ['py39']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 (
@@ -145,7 +146,7 @@ exclude = [
     "setup.py",
 ]
 line-length = 120
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 ignore = [

src/spatialdata/_core/_deepcopy.py

@@ -7,9 +7,8 @@
 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

src/spatialdata/_core/centroids.py

@@ -7,10 +7,9 @@
 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."
         )

src/spatialdata/_core/concatenate.py

@@ -52,7 +52,7 @@ 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
@@ -247,7 +247,7 @@ 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

src/spatialdata/_core/data_extent.py

@@ -8,10 +8,9 @@
 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)
 
 

src/spatialdata/_core/operations/_utils.py

@@ -2,8 +2,7 @@
 
 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,

src/spatialdata/_core/operations/aggregate.py

@@ -10,11 +10,10 @@
 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:

src/spatialdata/_core/operations/map.py

@@ -1,13 +1,12 @@
 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.transformations import get_transformation

src/spatialdata/_core/operations/rasterize.py

@@ -5,10 +5,9 @@
 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

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 channel_rasterization(block_id: tuple[int, int, int] | None) -> ArrayLike:
             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:

src/spatialdata/_core/operations/transform.py

@@ -10,10 +10,9 @@
 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
@@ -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:
@@ -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, ...