Merge pull request #337 from campaslab/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.5.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: ^\.napari-hub/.*
       - id: check-yaml # checks for correct yaml syntax for github actions ex.
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.256
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.5
     hooks:
       - id: ruff
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.11.0
     hooks:
       - id: black
   - repo: https://github.com/tlambert03/napari-plugin-checks

src/napari_stress/_measurements/geodesics.py

@@ -138,7 +138,6 @@ def correlation_on_surface(
 
     # calculate autocorrelation with spatially averaged feature values
     for dist_i in range(0, maximal_distance + 1):
-
         sum_mean_curv_corr_d_i, n_points = _avg_around_pt(
             dist_i, dists_lbdv_non0, Corr_non0_pts, maximal_distance
         )
@@ -235,7 +234,6 @@ def local_extrema_analysis(
     delta_feature_nearest_min_max = np.zeros_like(feature)
 
     for pt in range(quad_fit):
-
         H_pt = feature[pt]
 
         # set to True, change if False:

src/napari_stress/_measurements/stresses.py

@@ -172,6 +172,7 @@ def calculate_anisotropy(
         every group in the dataframe
 
     """
+
     # write a function to apply to every group in the dataframe
     def anisotropy(
         df: pd.DataFrame, alpha: float = 0.05, column: str = "anisotropic_stress"

src/napari_stress/_reconstruction/reconstruct_surface.py

@@ -46,7 +46,6 @@ def reconstruct_surface_from_quadrature_points(points: PointsData) -> SurfaceDat
             vertex = tetras[tri_i, tetra_vert]
 
             if vertex != n_quadrature_points and vert_ind < 3:
-
                 delauney_triangles[tri_i, vert_ind] = vertex
                 vert_ind = vert_ind + 1
 

src/napari_stress/_reconstruction/refine_surfaces.py

@@ -147,7 +147,6 @@ def trace_refinement_of_surface(
 
     # Iterate over all provided target points
     for idx in range(n_points):
-
         array = np.array(intensity_along_vector.loc[idx].to_numpy())
         # Simple or fancy fit?
         if selected_fit_type == fit_types.quick_edge_fit:
@@ -329,7 +328,6 @@ def _fancy_edge_fit(
     array = [x for x in array if not np.isnan(x)]  # filter out nans
     try:
         if selected_edge_func == _sigmoid:
-
             # trim begin of trace to get rid of rising intensity slope
             ind_max = np.argmax(array)
             array = array[ind_max:]

src/napari_stress/_spherical_harmonics/spherical_harmonics.py

@@ -55,7 +55,6 @@ def shtools_spherical_harmonics_expansion(
     longitude = np.rad2deg(spherical_coordinates[2])
 
     if expansion_type == "radial":
-
         # Find spherical harmonics expansion coefficients until specified degree
         opt_fit_params = pyshtools._SHTOOLS.SHExpandLSQ(
             radius, latitude, longitude, lmax=max_degree
@@ -74,7 +73,6 @@ def shtools_spherical_harmonics_expansion(
         return points, coefficients
 
     elif expansion_type == "cartesian":
-
         optimal_fit_params = []
         fitted_coordinates = np.zeros_like(points)
         for i in range(3):
@@ -267,7 +265,6 @@ def lebedev_quadrature(
 def create_manifold(
     points: PointsData, lebedev_fit: lebedev_info.lbdv_info, max_degree: int
 ) -> mnfd.manifold:
-
     # add information to manifold on what type of expansion was used
     Manny_Dict = {}
     Manny_Name_Dict = {}  # sph point cloud at lbdv

src/napari_stress/_stress/charts_SPB.py

@@ -14,7 +14,6 @@
 
 def Domain(Theta, Phi):  # Which coordinates to use
     if Chart_Min_Polar <= Phi and Phi <= Chart_Max_Polar:  # Use Coordinates A
-
         Bar_Coors = Coor_A_To_B(Theta, Phi)
         Phi_Bar = Bar_Coors[1]
 
@@ -32,7 +31,6 @@ def Domain(Theta, Phi):  # Which coordinates to use
 
 def Domain_Unaffected(Theta, Phi):  # Where fns in each chart arent affected by eta fns
     if eta_Min_Polar <= Phi and Phi <= eta_Max_Polar:  # Use Coordinates A
-
         Bar_Coors = Coor_A_To_B(Theta, Phi)
         Phi_Bar = Bar_Coors[1]
 
@@ -97,7 +95,6 @@ def eta_A_const(
 def eta_B(
     func, Theta_Bar, Phi_Bar
 ):  # Cutoff fn for Phi_Bar in [eta_Min_Polar, eta_Max_Polar]
-
     # func needs to be COUNTER rotated back to phi, theta, to be consistent
     def func_counter_rot(theta_bar, phi_bar):
         Orig_Coors = Coor_B_To_A(theta_bar, phi_bar)
@@ -111,7 +108,6 @@ def func_counter_rot(theta_bar, phi_bar):
 # NOTE: (Theta, Phi) ->
 # (Theta_Bar, Phi_Bar) by rotating the north pole (0,0) to the east pole (0,pi/2)
 def Coor_A_To_B(Theta, Phi):  # Converts from A to B
-
     X1 = np.cos(Theta) * np.sin(Phi)
     Y1 = np.sin(Theta) * np.sin(Phi)
     Z1 = np.cos(Phi)
@@ -141,7 +137,6 @@ def Coor_A_To_B(Theta, Phi):  # Converts from A to B
 
 
 def Coor_B_To_A(Theta_Bar, Phi_Bar):  # Converts from B back to A
-
     # X2 = cos(Theta_Bar)*sin(Phi_Bar)
     # Y2 = sin(Theta_Bar)*sin(Phi_Bar)
     # Z2 = cos(Phi_Bar)
@@ -173,14 +168,12 @@ def Coor_B_To_A(Theta_Bar, Phi_Bar):  # Converts from B back to A
 
 # Uses F(theta, phi) to find F_{Rot}(theta_bar, phi_bar)
 def Rotate_Fn(func, Theta_Bar, Phi_Bar):
-
     Theta, Phi = Coor_B_To_A(Theta_Bar, Phi_Bar)
     return func(Theta, Phi)
 
 
 # (x,y,z) -> (theta, phi)
 def Cart_To_Coor_A(x, y, z):
-
     r = np.sqrt(pow(x, 2) + pow(y, 2) + pow(z, 2))
 
     ##Calculate Theta
@@ -200,7 +193,6 @@ def Cart_To_Coor_A(x, y, z):
 
 # (x,y,z) -> (theta_bar, phi_bar)
 def Cart_To_Coor_B(x, y, z):
-
     r = np.sqrt(pow(x, 2) + pow(y, 2) + pow(z, 2))
 
     ##Calculate Theta_Bar