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

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

Author: pre-commit-ci[bot]

src/napari_stress/_approximation/expansion.py

@@ -1,6 +1,7 @@
-import numpy as np
 from typing import TYPE_CHECKING
 
+import numpy as np
+
 if TYPE_CHECKING:
     import napari
 

src/napari_stress/_approximation/expansion_base.py

@@ -1,5 +1,6 @@
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     import napari
 

src/napari_stress/_approximation/expansion_napari.py

@@ -1,5 +1,7 @@
-from napari_tools_menu import register_function
 from typing import TYPE_CHECKING
+
+from napari_tools_menu import register_function
+
 if TYPE_CHECKING:
     import napari
 

src/napari_stress/_approximation/fit_ellipsoid.py

@@ -1,13 +1,15 @@
+from typing import TYPE_CHECKING
+
 import deprecation
 import numpy as np
 from napari.types import PointsData, VectorsData
 from napari_tools_menu import register_function
-from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     import napari
 
-from .._version import __version__
 from .._utils.frame_by_frame import frame_by_frame
+from .._version import __version__
 
 
 @deprecation.deprecated(

src/napari_stress/_measurements/curvature.py

@@ -1,3 +1,5 @@
+from typing import TYPE_CHECKING
+
 import numpy as np
 import pandas as pd
 from napari.layers import Layer
@@ -23,7 +25,6 @@
     manifold,
 )
 
-from typing import TYPE_CHECKING
 if TYPE_CHECKING:
     import napari
 
@@ -256,7 +257,8 @@ def calculate_patch_fitted_curvature_on_pointcloud(
     df = pd.DataFrame(
         {
             "mean_curvature": mean_curvatures,
-            "gaussian_curvature": principal_curvatures[:, 0] * principal_curvatures[:, 1],
+            "gaussian_curvature": principal_curvatures[:, 0]
+            * principal_curvatures[:, 1],
             "principal_curvature_1": principal_curvatures[:, 0],
             "principal_curvature_2": principal_curvatures[:, 1],
         }
@@ -384,7 +386,9 @@ def calculate_mean_curvature_on_manifold(
 
     # Makre sure orientation is inward,
     # so H is positive (for Ellipsoid, and small deviations):
-    Orientations = [np.dot(x, y) for x, y in zip(centered_lbdv_pts, normals)]
+    Orientations = [
+        np.dot(x, y) for x, y in zip(centered_lbdv_pts, normals, strict=False)
+    ]
     num_pos_orr = np.sum(np.asarray(Orientations).flatten() > 0)
 
     Orientation = 1.0  # unchanged (we want INWARD)

src/napari_stress/_measurements/geodesics.py

@@ -1,10 +1,11 @@
+from typing import TYPE_CHECKING
+
 import numpy as np
 from napari.types import LayerDataTuple, SurfaceData
 from napari_tools_menu import register_function
 
 from .._utils.frame_by_frame import frame_by_frame
 
-from typing import TYPE_CHECKING
 if TYPE_CHECKING:
     import napari
 
@@ -28,6 +29,7 @@ def geodesic_distance_matrix(surface: SurfaceData) -> np.ndarray:
 
     """
     import gdist
+
     from .._utils import sanitize_faces
 
     # Reorder the faces of the surface to ensure consistent orientation
@@ -36,7 +38,8 @@ def geodesic_distance_matrix(surface: SurfaceData) -> np.ndarray:
     faces = sanitized_surface[1]
 
     distance_matrix = gdist.local_gdist_matrix(
-        vertices, faces, max_distance=1e9).toarray()
+        vertices, faces, max_distance=1e9
+    ).toarray()
 
     return distance_matrix
 
@@ -66,6 +69,7 @@ def geodesic_path(
 
     """
     import potpourri3d as pp3d
+
     from .._utils import sanitize_faces
 
     sanitized_surface = sanitize_faces(surface)
@@ -234,6 +238,7 @@ def local_extrema_analysis(
             - `min_max_pair_anisotropies`: Difference in input value `(vertices, faces, values)` between all pairs of local minima and maxima.
     """
     from .._utils import sanitize_faces
+
     feature = surface[2]
     surface = sanitize_faces(surface)
     triangles = surface[1]

src/napari_stress/_measurements/intensity.py

@@ -1,13 +1,16 @@
+from typing import TYPE_CHECKING
+
 import numpy as np
 import pandas as pd
 from napari.types import LayerDataTuple
 from napari_tools_menu import register_function
 
 from .._utils.frame_by_frame import frame_by_frame
-from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     import napari
 
+
 @register_function(
     menu="Measurement > Measure intensities on surface (n-STRESS)"
 )

src/napari_stress/_measurements/stresses.py

@@ -1,4 +1,5 @@
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     import napari
 

src/napari_stress/_measurements/toolbox.py

@@ -3,7 +3,7 @@
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    import napari
+    pass
 
 import numpy as np
 from magicgui.widgets import create_widget
@@ -597,9 +597,7 @@ def comprehensive_analysis(
 
     GDM = None
     if GDM is None:
-        GDM = measurements.geodesic_distance_matrix(
-            surface_cell_stress
-        )
+        GDM = measurements.geodesic_distance_matrix(surface_cell_stress)
 
     if maximal_distance is None:
         maximal_distance = int(np.floor(np.nanmax(GDM[np.inf != GDM])))

src/napari_stress/_reconstruction/fit_utils.py

@@ -1,6 +1,7 @@
 import inspect
 from enum import Enum
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     import napari