fix pip installation problems due to xarray-dataclasses (#967)

* constrain xarray

* fix pre-commit, allow python3.13, update xarray-dataclass dep

* remove xarray-constraint

* update spatial image dependency and msi, remove xarray-dataclass dep

* revert type ngff_transformations

* add mypy ignore

* fix

---------

Co-authored-by: Wouter-Michiel Vierdag <[email protected]>

Author: LucaMarconato

.mypy.ini

@@ -1,6 +1,5 @@
 [mypy]
 python_version = 3.10
-plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
 warn_redundant_casts = True

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 = ">=3.10, <3.13" # include 3.13 once multiscale-spatial-image conflicts are resolved
+requires-python = ">=3.10"
 dynamic= [
   "version" # allow version to be set by git tags
 ]
@@ -29,7 +29,7 @@ dependencies = [
     "datashader",
     "fsspec",
     "geopandas>=0.14",
-    "multiscale_spatial_image>=2.0.2",
+    "multiscale_spatial_image>=2.0.3",
     "networkx",
     "numba>=0.55.0",
     "numpy",
@@ -40,14 +40,13 @@ dependencies = [
     "rich",
     "setuptools",
     "shapely>=2.0.1",
-    "spatial_image>=1.1.0",
+    "spatial_image>=1.2.3",
     "scikit-image",
     "scipy",
     "typing_extensions>=4.8.0",
     "xarray>=2024.10.0",
     "xarray-schema",
     "xarray-spatial>=0.3.5",
-	"xarray-dataclasses>=1.8.0",
     "zarr<3",
 ]
 

src/spatialdata/transformations/ngff/ngff_transformations.py

@@ -340,7 +340,7 @@ def transform_points(self, points: ArrayLike) -> ArrayLike:
         self._validate_transform_points_shapes(len(input_axes), points.shape)
         p = np.vstack([points.T, np.ones(points.shape[0])])
         q = self.affine @ p
-        return q[: len(output_axes), :].T
+        return q[: len(output_axes), :].T  # type: ignore[no-any-return]
 
     def to_affine(self) -> "NgffAffine":
         return NgffAffine(
@@ -744,7 +744,7 @@ def _get_and_validate_axes(self) -> tuple[tuple[str, ...], tuple[str, ...]]:
     def transform_points(self, points: ArrayLike) -> ArrayLike:
         input_axes, _ = self._get_and_validate_axes()
         self._validate_transform_points_shapes(len(input_axes), points.shape)
-        return (self.rotation @ points.T).T
+        return (self.rotation @ points.T).T  # type: ignore[no-any-return]
 
     def to_affine(self) -> NgffAffine:
         m = np.eye(len(self.rotation) + 1)