[pre-commit.ci] pre-commit autoupdate (scverse#685)

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.7...v0.6.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update pre-commit

* fix precommit

---------

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

.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.7
+      rev: v0.6.2
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

src/spatialdata/_core/operations/rasterize.py

@@ -336,7 +336,7 @@ def rasterize(
             element_name = data if isinstance(data, str) else None
             kwargs = {"sdata": sdata, "element_name": element_name} if element_name is not None else {"element": data}
             values = get_values(value_key, table_name=table_name, **kwargs).iloc[:, 0]  # type: ignore[arg-type, union-attr]
-            max_index = np.max(values.index)
+            max_index: int = np.max(values.index)
             assigner = np.zeros(max_index + 1, dtype=values.dtype)
             assigner[values.index] = values
             # call-arg is ignored because model is never TableModel (the error is that the transformation param is not

src/spatialdata/_core/operations/rasterize_bins.py

@@ -14,6 +14,7 @@
 from xarray import DataArray
 
 from spatialdata._core.query.relational_query import get_values
+from spatialdata._types import ArrayLike
 from spatialdata.models import Image2DModel, get_table_keys
 from spatialdata.transformations import Affine, Sequence, get_transformation
 
@@ -113,8 +114,9 @@ def rasterize_bins(
     if value_key is None:
         shape = (n_rows, n_cols)
 
-        def channel_rasterization(block_id: tuple[int, int, int] | None) -> np.ndarray:  # type: ignore[type-arg]
-            image = np.zeros((1, *shape), dtype=dtype)
+        def channel_rasterization(block_id: tuple[int, int, int] | None) -> ArrayLike:
+
+            image: ArrayLike = np.zeros((1, *shape), dtype=dtype)
 
             if block_id is None:
                 return image

src/spatialdata/_core/operations/transform.py

@@ -49,11 +49,11 @@ def _transform_raster(
     v: ArrayLike = np.hstack(c_channel + [binary, np.ones(len(binary)).reshape((-1, 1))])
     matrix = transformation.to_affine_matrix(input_axes=axes, output_axes=axes)
     inverse_matrix = transformation.inverse().to_affine_matrix(input_axes=axes, output_axes=axes)
-    new_v = (matrix @ v.T).T
+    new_v: ArrayLike = (matrix @ v.T).T
     c_shape: tuple[int, ...]
     c_shape = (data.shape[0],) if "c" in axes else ()
     new_spatial_shape = tuple(
-        int(np.max(new_v[:, i]) - np.min(new_v[:, i])) for i in range(len(c_shape), n_spatial_dims + len(c_shape))
+        int(np.max(new_v[:, i]) - np.min(new_v[:, i])) for i in range(len(c_shape), n_spatial_dims + len(c_shape))  # type: ignore[operator]
     )
     output_shape = c_shape + new_spatial_shape
     translation_vector = np.min(new_v[:, :-1], axis=0)

tests/conftest.py

@@ -21,6 +21,8 @@
 from shapely import linearrings, polygons
 from shapely.geometry import MultiPolygon, Point, Polygon
 from skimage import data
+from xarray import DataArray
+
 from spatialdata._core._deepcopy import deepcopy
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
@@ -34,7 +36,6 @@
     ShapesModel,
     TableModel,
 )
-from xarray import DataArray
 
 SEED = 0
 RNG = default_rng(seed=SEED)

tests/core/operations/test_aggregations.py

@@ -8,6 +8,7 @@
 from anndata.tests.helpers import assert_equal
 from geopandas import GeoDataFrame
 from numpy.random import default_rng
+
 from spatialdata import aggregate, to_polygons
 from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata._core.spatialdata import SpatialData

tests/core/operations/test_map.py

@@ -2,9 +2,10 @@
 
 import numpy as np
 import pytest
+from xarray import DataArray
+
 from spatialdata._core.operations.map import map_raster
 from spatialdata.transformations import Translation, get_transformation, set_transformation
-from xarray import DataArray
 
 
 def _multiply(arr, parameter=10):

tests/core/operations/test_rasterize.py

@@ -11,15 +11,15 @@
 from multiscale_spatial_image import MultiscaleSpatialImage
 from shapely import MultiPolygon, box
 from spatial_image import SpatialImage
+from xarray import DataArray
+
 from spatialdata import SpatialData, get_extent
 from spatialdata._core.operations.rasterize import rasterize
 from spatialdata._core.query.relational_query import get_element_instances
 from spatialdata._io._utils import _iter_multiscale
 from spatialdata.models import PointsModel, ShapesModel, TableModel, get_axes_names
 from spatialdata.models._utils import get_spatial_axes
 from spatialdata.transformations import MapAxis
-from xarray import DataArray
-
 from tests.conftest import _get_images, _get_labels
 
 

tests/core/operations/test_rasterize_bins.py

@@ -8,6 +8,7 @@
 from pandas import DataFrame
 from scipy.sparse import csr_matrix
 from shapely.geometry import Polygon
+
 from spatialdata._core.data_extent import are_extents_equal, get_extent
 from spatialdata._core.operations.rasterize_bins import rasterize_bins
 from spatialdata._core.spatialdata import SpatialData

tests/core/operations/test_spatialdata_operations.py

@@ -5,6 +5,7 @@
 import numpy as np
 import pytest
 from anndata import AnnData
+
 from spatialdata._core.concatenate import _concatenate_tables, concatenate
 from spatialdata._core.data_extent import are_extents_equal, get_extent
 from spatialdata._core.operations._utils import transform_to_data_extent
@@ -21,7 +22,6 @@
     Sequence,
     Translation,
 )
-
 from tests.conftest import _get_table
 
 

tests/core/operations/test_transform.py

@@ -6,6 +6,8 @@
 import pytest
 from datatree import DataTree
 from geopandas.testing import geom_almost_equals
+from xarray import DataArray
+
 from spatialdata import transform
 from spatialdata._core.data_extent import are_extents_equal, get_extent
 from spatialdata._core.spatialdata import SpatialData
@@ -28,7 +30,6 @@
     Sequence,
     Translation,
 )
-from xarray import DataArray
 
 
 class TestElementsTransform:

tests/core/operations/test_vectorize.py

@@ -4,6 +4,7 @@
 import pytest
 from geopandas import GeoDataFrame
 from shapely import MultiPoint, Point
+
 from spatialdata._core.operations.vectorize import to_circles, to_polygons
 from spatialdata.datasets import blobs
 from spatialdata.models.models import ShapesModel

tests/core/query/test_relational_query.py

@@ -2,6 +2,7 @@
 import pandas as pd
 import pytest
 from anndata import AnnData
+
 from spatialdata import get_values, match_table_to_element
 from spatialdata._core.query.relational_query import (
     _locate_value,

tests/core/query/test_spatial_query.py

@@ -11,6 +11,8 @@
 from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import MultiPolygon, Point, Polygon
+from xarray import DataArray
+
 from spatialdata._core.data_extent import get_extent
 from spatialdata._core.query.spatial_query import (
     BaseSpatialRequest,
@@ -30,8 +32,6 @@
 )
 from spatialdata.testing import assert_spatial_data_objects_are_identical
 from spatialdata.transformations import Identity, MapAxis, set_transformation
-from xarray import DataArray
-
 from tests.conftest import _make_points, _make_squares
 
 

tests/core/test_centroids.py

@@ -5,6 +5,7 @@
 import pytest
 from anndata import AnnData
 from numpy.random import default_rng
+
 from spatialdata._core.centroids import get_centroids
 from spatialdata._core.query.relational_query import get_element_instances
 from spatialdata.models import Labels2DModel, Labels3DModel, PointsModel, TableModel, get_axes_names

tests/core/test_data_extent.py

@@ -6,6 +6,7 @@
 from geopandas import GeoDataFrame
 from numpy.random import default_rng
 from shapely.geometry import MultiPolygon, Point, Polygon
+
 from spatialdata import SpatialData, get_extent, transform
 from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata.datasets import blobs

tests/core/test_deepcopy.py

@@ -1,4 +1,5 @@
 from pandas.testing import assert_frame_equal
+
 from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata.testing import assert_spatial_data_objects_are_identical
 

tests/dataloader/test_datasets.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 from spatialdata.dataloader import ImageTilesDataset
 from spatialdata.datasets import blobs_annotating_element
 

tests/io/test_format.py

@@ -2,6 +2,7 @@
 
 import pytest
 from shapely import GeometryType
+
 from spatialdata._io.format import CurrentPointsFormat, CurrentShapesFormat, ShapesFormatV01
 from spatialdata.models import PointsModel, ShapesModel
 

tests/io/test_metadata.py

@@ -3,6 +3,7 @@
 import tempfile
 
 import pytest
+
 from spatialdata import SpatialData, read_zarr
 from spatialdata._io._utils import _is_element_self_contained
 from spatialdata._logging import logger

tests/io/test_multi_table.py

@@ -4,9 +4,9 @@
 import pytest
 from anndata import AnnData
 from anndata.tests.helpers import assert_equal
+
 from spatialdata import SpatialData, concatenate
 from spatialdata.models import TableModel
-
 from tests.conftest import _get_shapes, _get_table
 
 # notes on paths: https://github.com/orgs/scverse/projects/17/views/1?pane=issue&itemId=44066734

tests/io/test_readwrite.py

@@ -8,6 +8,7 @@
 import pytest
 from anndata import AnnData
 from numpy.random import default_rng
+
 from spatialdata import SpatialData, deepcopy, read_zarr
 from spatialdata._io._utils import _are_directories_identical, get_dask_backing_files
 from spatialdata.datasets import blobs
@@ -19,7 +20,6 @@
     set_transformation,
 )
 from spatialdata.transformations.transformations import Identity, Scale
-
 from tests.conftest import _get_images, _get_labels, _get_points, _get_shapes
 
 RNG = default_rng(0)

tests/io/test_utils.py

@@ -2,6 +2,7 @@
 import tempfile
 
 import dask.dataframe as dd
+
 from spatialdata import read_zarr
 from spatialdata._io._utils import get_dask_backing_files
 

tests/models/test_models.py

@@ -22,6 +22,8 @@
 from shapely.geometry import MultiPolygon, Point, Polygon
 from shapely.io import to_ragged_array
 from spatial_image import to_spatial_image
+from xarray import DataArray
+
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
 from spatialdata.models._utils import (
@@ -51,8 +53,6 @@
     set_transformation,
 )
 from spatialdata.transformations.transformations import Identity, Scale
-from xarray import DataArray
-
 from tests.conftest import (
     MULTIPOLYGON_PATH,
     POINT_PATH,

tests/transformations/ngff/test_ngff_coordinate_system.py

@@ -2,6 +2,7 @@
 import json
 
 import pytest
+
 from spatialdata.transformations.ngff.ngff_coordinate_system import (
     NgffAxis,
     NgffCoordinateSystem,

tests/transformations/ngff/test_ngff_transformations.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 import pytest
+
 from spatialdata._types import ArrayLike
 from spatialdata.models import C, X, Y, Z
 from spatialdata.transformations.ngff._utils import get_default_coordinate_system
@@ -19,7 +20,6 @@
     NgffSequence,
     NgffTranslation,
 )
-
 from tests.transformations.ngff.conftest import (
     c_cs,
     cyx_cs,

tests/transformations/test_transformations.py

@@ -4,6 +4,8 @@
 import numpy as np
 import pytest
 import xarray.testing
+from xarray import DataArray
+
 from spatialdata import transform
 from spatialdata.datasets import blobs
 from spatialdata.models import Image2DModel, PointsModel
@@ -32,7 +34,6 @@
     _decompose_transformation,
     _get_affine_for_element,
 )
-from xarray import DataArray
 
 
 def test_identity():

tests/utils/test_element_utils.py

@@ -4,10 +4,11 @@
 import pytest
 import xarray
 from datatree import DataTree
+from xarray import DataArray
+
 from spatialdata._utils import unpad_raster
 from spatialdata.models import get_model
 from spatialdata.transformations import Affine
-from xarray import DataArray
 
 
 def _pad_raster(data: DataArray, axes: tuple[str, ...]) -> DataArray:

tests/utils/test_testing.py

@@ -3,6 +3,8 @@
 import numpy as np
 import pytest
 from datatree import DataTree
+from xarray import DataArray
+
 from spatialdata import SpatialData, deepcopy
 from spatialdata.models import (
     Image2DModel,
@@ -16,7 +18,6 @@
 )
 from spatialdata.testing import assert_elements_are_identical, assert_spatial_data_objects_are_identical
 from spatialdata.transformations import Scale, set_transformation
-from xarray import DataArray
 
 scale = Scale([1.0], axes=("x",))