[pre-commit.ci] pre-commit autoupdate (#638)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/mirrors-mypy: v1.10.1 → v1.11.0](pre-commit/mirrors-mypy@v1.10.1...v1.11.0)
- [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.5.4](astral-sh/ruff-pre-commit@v0.5.1...v0.5.4)

* fix pre-commit

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Luca Marconato <[email protected]>

.pre-commit-config.yaml

@@ -21,13 +21,13 @@ repos:
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.10.1
+      rev: v1.11.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.1
+      rev: v0.5.4
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

src/spatialdata/testing.py

@@ -95,7 +95,7 @@ def assert_elements_are_identical(
     Please see
     :func:`spatialdata.testing.assert_spatial_data_objects_are_identical` for additional comments.
     """
-    assert type(element0) == type(element1)
+    assert type(element0) is type(element1)
     if check_transformations and not check_metadata:
         raise ValueError("check_transformations cannot be True if check_metadata is False")
 

src/spatialdata/transformations/ngff/ngff_transformations.py

@@ -414,7 +414,7 @@ def transform_points(self, points: ArrayLike) -> ArrayLike:
         new_indices = [input_axes.index(self.map_axis[ax]) for ax in output_axes]
         assert len(new_indices) == len(output_axes)
         mapped = points[:, new_indices]
-        assert type(mapped) == np.ndarray
+        assert isinstance(mapped, np.ndarray)
         return mapped
 
     def to_affine(self) -> NgffAffine:
@@ -888,7 +888,7 @@ def _inferring_cs_pre_action(
             if expected_output_cs is not None:
                 assert t.output_coordinate_system == expected_output_cs
         new_latest_output_cs = t.output_coordinate_system
-        assert type(new_latest_output_cs) == NgffCoordinateSystem
+        assert isinstance(new_latest_output_cs, NgffCoordinateSystem)
         return new_latest_output_cs, input_cs, output_cs
 
     @staticmethod

tests/io/test_readwrite.py

@@ -296,14 +296,14 @@ def test_replace_transformation_on_disk_raster(self, images, labels):
                     f = os.path.join(td, "data.zarr")
                     single_sdata.write(f)
                     t0 = get_transformation(SpatialData.read(f)[elem_name])
-                    assert type(t0) == Identity
+                    assert isinstance(t0, Identity)
                     set_transformation(
                         single_sdata[elem_name],
                         Scale([2.0], axes=("x",)),
                         write_to_sdata=single_sdata,
                     )
                     t1 = get_transformation(SpatialData.read(f)[elem_name])
-                    assert type(t1) == Scale
+                    assert isinstance(t1, Scale)
 
     def test_replace_transformation_on_disk_non_raster(self, shapes, points):
         sdatas = {"shapes": shapes, "points": points}
@@ -314,10 +314,10 @@ def test_replace_transformation_on_disk_non_raster(self, shapes, points):
                 f = os.path.join(td, "data.zarr")
                 sdata.write(f)
                 t0 = get_transformation(SpatialData.read(f).__getattribute__(k)[elem_name])
-                assert type(t0) == Identity
+                assert isinstance(t0, Identity)
                 set_transformation(sdata[elem_name], Scale([2.0], axes=("x",)), write_to_sdata=sdata)
                 t1 = get_transformation(SpatialData.read(f)[elem_name])
-                assert type(t1) == Scale
+                assert isinstance(t1, Scale)
 
     def test_overwrite_works_when_no_zarr_store(self, full_sdata):
         with tempfile.TemporaryDirectory() as tmpdir: