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

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

.scripts/ci/download_data.py

@@ -30,9 +30,10 @@ def _maybe_download_data(func_name: str, path: Path) -> Any:
 
 
 def main(args: argparse.Namespace) -> None:
-    import squidpy as sq
     from anndata import AnnData
 
+    import squidpy as sq
+
     all_datasets = sq.datasets._dataset.__all__ + sq.datasets._image.__all__
     all_extensions = ["h5ad"] * len(sq.datasets._dataset.__all__) + ["tiff"] * len(sq.datasets._image.__all__)
 

tests/conftest.py

@@ -18,12 +18,13 @@
 import pytest
 import scanpy as sc
 import spatialdata as sd
-import squidpy as sq
 from anndata import AnnData, OldFormatWarning
 from geopandas import GeoDataFrame
 from matplotlib.testing.compare import compare_images
 from scipy.sparse import csr_matrix
 from shapely import LineString, Point, Polygon, distance
+
+import squidpy as sq
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr import spatial_neighbors
 from squidpy.im._container import ImageContainer

tests/datasets/test_dataset.py

@@ -6,9 +6,10 @@
 from types import FunctionType
 
 import pytest
-import squidpy as sq
 from anndata import AnnData, OldFormatWarning
 
+import squidpy as sq
+
 
 class TestDatasetsImports:
     @pytest.mark.parametrize("func", sq.datasets._dataset.__all__ + sq.datasets._image.__all__)

tests/datasets/test_download_visium_dataset.py

@@ -10,6 +10,7 @@
 import pytest
 from anndata.tests.helpers import assert_adata_equal
 from scanpy._settings import settings
+
 from squidpy.datasets import visium
 
 

tests/graph/test_ligrec.py

@@ -14,6 +14,7 @@
 from pandas.testing import assert_frame_equal
 from scanpy import settings as s
 from scanpy.datasets import blobs
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr import ligrec
 from squidpy.gr._ligrec import PermutationTest

tests/graph/test_nhood.py

@@ -4,6 +4,7 @@
 import pandas as pd
 import pytest
 from anndata import AnnData
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr import (
     centrality_scores,

tests/graph/test_ppatterns.py

@@ -6,6 +6,7 @@
 import pytest
 from anndata import AnnData
 from pandas.testing import assert_frame_equal
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr import co_occurrence, spatial_autocorr
 from squidpy.gr._ppatterns import _find_min_max

tests/graph/test_ripley.py

@@ -3,6 +3,7 @@
 import numpy as np
 import pytest
 from anndata import AnnData
+
 from squidpy._constants._constants import RipleyStat
 from squidpy.gr import ripley
 

tests/graph/test_sepal.py

@@ -3,6 +3,7 @@
 import numpy as np
 from anndata import AnnData
 from pandas.testing import assert_frame_equal
+
 from squidpy.gr import sepal, spatial_neighbors
 
 UNS_KEY = "sepal_score"

tests/graph/test_spatial_neighbors.py

@@ -9,6 +9,7 @@
 from scipy.sparse import isspmatrix_csr
 from shapely import Point
 from spatialdata.datasets import blobs
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr import mask_graph, spatial_neighbors
 from squidpy.gr._build import _build_connectivity

tests/graph/test_utils.py

@@ -4,6 +4,7 @@
 import pandas as pd
 import pytest
 from anndata import AnnData
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr._utils import _shuffle_group
 

tests/image/test_container.py

@@ -13,12 +13,13 @@
 import imageio.v3 as iio
 import numpy as np
 import pytest
-import squidpy as sq
 import tifffile
 import xarray as xr
 from anndata import AnnData
 from PIL import Image
 from pytest_mock import MockerFixture
+
+import squidpy as sq
 from squidpy._constants._pkg_constants import Key
 from squidpy.im import ImageContainer
 from squidpy.im._coords import _NULL_COORDS, CropCoords, CropPadding

tests/image/test_features.py

@@ -7,6 +7,7 @@
 import pytest
 from anndata import AnnData
 from pytest_mock import MockerFixture
+
 from squidpy._constants._constants import ImageFeature
 from squidpy.im._container import ImageContainer
 from squidpy.im._feature import calculate_image_features

tests/image/test_io.py

@@ -7,6 +7,7 @@
 import xarray as xr
 from pytest_mock import MockerFixture
 from skimage.io import imread
+
 from squidpy._constants._constants import InferDimensions
 from squidpy.im._io import _get_image_shape_dtype, _infer_dimensions, _lazy_load_image
 

tests/image/test_processing.py

@@ -6,6 +6,7 @@
 import numpy as np
 import pytest
 from pytest_mock import MockerFixture
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.im import ImageContainer, process
 

tests/image/test_segmentation.py

@@ -6,6 +6,7 @@
 import numpy as np
 import pytest
 from pytest_mock import MockerFixture
+
 from squidpy._constants._constants import SegmentationBackend
 from squidpy._constants._pkg_constants import Key
 from squidpy.im import (

tests/plotting/test_graph.py

@@ -9,8 +9,8 @@
 import pytest
 import scanpy as sc
 from anndata import AnnData
-from squidpy import gr, pl
 
+from squidpy import gr, pl
 from tests.conftest import DPI, PlotTester, PlotTesterMeta
 
 C_KEY = "leiden"

tests/plotting/test_image.py

@@ -5,11 +5,11 @@
 import pandas as pd
 import pytest
 import scanpy as sc
-import squidpy as sq
 from anndata import AnnData
 from matplotlib.testing.compare import compare_images
-from squidpy.im import ImageContainer
 
+import squidpy as sq
+from squidpy.im import ImageContainer
 from tests.conftest import ACTUAL, DPI, EXPECTED, TOL, PlotTester, PlotTesterMeta
 
 

tests/plotting/test_interactive.py

@@ -10,8 +10,8 @@
 from matplotlib.testing.compare import compare_images
 from scanpy import settings as s
 from scipy.sparse import issparse
-from squidpy.im import ImageContainer
 
+from squidpy.im import ImageContainer
 from tests.conftest import ACTUAL, DPI, EXPECTED, TOL, PlotTester, PlotTesterMeta
 
 

tests/plotting/test_spatial_static.py

@@ -11,11 +11,11 @@
 import scanpy as sc
 from anndata import AnnData
 from matplotlib.colors import ListedColormap
+
 from squidpy import pl
 from squidpy._constants._pkg_constants import Key
 from squidpy.gr import spatial_neighbors
 from squidpy.pl._spatial_utils import _get_library_id
-
 from tests.conftest import PlotTester, PlotTesterMeta
 
 sc.set_figure_params(dpi=40, color_map="viridis")

tests/plotting/test_var_by_distance_plot.py

@@ -2,8 +2,8 @@
 
 import scanpy as sc
 from anndata import AnnData
-from squidpy import pl, tl
 
+from squidpy import pl, tl
 from tests.conftest import PlotTester, PlotTesterMeta
 
 sc.pl.set_rcParams_defaults()

tests/read/test_visium.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from anndata.tests.helpers import assert_adata_equal
+
 from squidpy._constants._pkg_constants import Key
 from squidpy.read import visium
 

tests/tools/test_var_by_distance.py

@@ -2,6 +2,7 @@
 
 import pytest
 from anndata import AnnData
+
 from squidpy.tl import var_by_distance
 from squidpy.tl._var_by_distance import _normalize_distances