Merge pull request #357 from campaslab/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate
campaslab · Apr 16, 2024 · be622dc · be622dc
2 parents 65e4663 + e00c8d5
commit be622dc
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Showing 9 changed files with 36 additions and 45 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     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/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.3.7
     hooks:
       - id: ruff
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.4.0
     hooks:
       - id: black
   - repo: https://github.com/tlambert03/napari-plugin-checks

diff --git a/src/napari_stress/_approximation/expansion.py b/src/napari_stress/_approximation/expansion.py
@@ -113,9 +113,7 @@ def _fit_ellipsoid_to_points(
         z = points[:, 2, np.newaxis]
 
         # Construct the design matrix for the ellipsoid equation
-        design_matrix = np.hstack(
-            (x**2, y**2, z**2, x * y, x * z, y * z, x, y, z)
-        )
+        design_matrix = np.hstack((x**2, y**2, z**2, x * y, x * z, y * z, x, y, z))
         column_of_ones = np.ones_like(x)  # Column vector of ones
 
         # Perform least squares fitting to solve for the coefficients

diff --git a/src/napari_stress/_measurements/curvature.py b/src/napari_stress/_measurements/curvature.py
@@ -93,9 +93,7 @@ def curvature_on_ellipsoid(
     k_upstairs = a0**2 * a1**2 * a2**2
     K_downstairs = (
         a0**2 * a1**2 * np.cos(V) ** 2
-        + a2**2
-        * (a1**2 * np.cos(U) ** 2 + a0**2 * np.sin(U) ** 2)
-        * np.sin(V) ** 2
+        + a2**2 * (a1**2 * np.cos(U) ** 2 + a0**2 * np.sin(U) ** 2) * np.sin(V) ** 2
     ) ** 2
     k = k_upstairs / K_downstairs.squeeze()
     k1 = H_ellps_pts + np.sqrt(H_ellps_pts**2 - k)

diff --git a/src/napari_stress/_reconstruction/__init__.py b/src/napari_stress/_reconstruction/__init__.py
@@ -8,6 +8,7 @@
 resampled by fitting patches to the surface and resampling the surface
 according to the fitted patches.
 """
+
 from .refine_surfaces import trace_refinement_of_surface, resample_pointcloud
 from .toolbox import reconstruct_droplet
 from .reconstruct_surface import reconstruct_surface_from_quadrature_points

diff --git a/src/napari_stress/_spherical_harmonics/spherical_harmonics.py b/src/napari_stress/_spherical_harmonics/spherical_harmonics.py
@@ -295,9 +295,9 @@ def create_manifold(
     Manny_Dict["Maniold_lbdv"] = lebedev_fit
 
     Manny_Dict["Manifold_SPH_deg"] = max_degree
-    Manny_Dict[
-        "use_manifold_name"
-    ] = False  # we are NOT using named shapes in these tests
+    Manny_Dict["use_manifold_name"] = (
+        False  # we are NOT using named shapes in these tests
+    )
     Manny_Dict["Maniold_Name_Dict"] = Manny_Name_Dict
 
     return mnfd.manifold(

diff --git a/src/napari_stress/_stress/euclidian_k_form_SPB.py b/src/napari_stress/_stress/euclidian_k_form_SPB.py
@@ -1701,12 +1701,12 @@ def Divergence_1_Form(self, lbdv, debug_mode=False):
                         A_inv_from_G_pt, dPhi_Vec_X_A_pt
                     )  # np.linalg.solve(A_Mat_pt, dPhi_Vec_X_A_pt)
 
-                    V_local_coors_theta_dtheta_V_A[
-                        quad_pt, 0
-                    ] = dTheta_Vec_X_local_coors_A_pt[0]
-                    V_local_coors_phi_dphi_V_A[
-                        quad_pt, 0
-                    ] = dPhi_Vec_X_local_coors_A_pt[1]
+                    V_local_coors_theta_dtheta_V_A[quad_pt, 0] = (
+                        dTheta_Vec_X_local_coors_A_pt[0]
+                    )
+                    V_local_coors_phi_dphi_V_A[quad_pt, 0] = (
+                        dPhi_Vec_X_local_coors_A_pt[1]
+                    )
 
                     neg_A_inv_A_theta = np.dot(
                         A_inv_from_G_pt, A_theta_Mat_pt
@@ -1766,12 +1766,12 @@ def Divergence_1_Form(self, lbdv, debug_mode=False):
                         B_Mat_pt, dPhi_Vec_X_B_pt
                     )
 
-                    V_local_coors_theta_dtheta_V_B[
-                        quad_pt, 0
-                    ] = dTheta_Vec_X_local_coors_B_pt[0]
-                    V_local_coors_phi_dphi_V_B[
-                        quad_pt, 0
-                    ] = dPhi_Vec_X_local_coors_B_pt[1]
+                    V_local_coors_theta_dtheta_V_B[quad_pt, 0] = (
+                        dTheta_Vec_X_local_coors_B_pt[0]
+                    )
+                    V_local_coors_phi_dphi_V_B[quad_pt, 0] = (
+                        dPhi_Vec_X_local_coors_B_pt[1]
+                    )
 
                     neg_B_inv_B_theta = -1.0 * np.linalg.solve(B_Mat_pt, B_theta_Mat_pt)
                     neg_B_inv_B_phi = -1.0 * np.linalg.solve(B_Mat_pt, B_phi_Mat_pt)

diff --git a/src/napari_stress/_stress/lebedev_info_SPB.py b/src/napari_stress/_stress/lebedev_info_SPB.py
@@ -527,18 +527,18 @@ def __init__(
                 (Max_SPH_Deg + 1, Max_SPH_Deg + 1, self.lbdv_quad_pts, 4)
             )
 
-            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[
-                :, :, :, 0
-            ] = self.SPH_Basis_Wt_At_Quad_Pts
-            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[
-                :, :, :, 1
-            ] = self.SPH_Basis_At_Quad_Pts
-            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[
-                :, :, :, 2
-            ] = self.SPH_Phi_Der_At_Quad_Pts
-            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[
-                :, :, :, 3
-            ] = self.SPH_Phi_Phi_Der_At_Quad_Pts
+            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[:, :, :, 0] = (
+                self.SPH_Basis_Wt_At_Quad_Pts
+            )
+            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[:, :, :, 1] = (
+                self.SPH_Basis_At_Quad_Pts
+            )
+            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[:, :, :, 2] = (
+                self.SPH_Phi_Der_At_Quad_Pts
+            )
+            To_Pickle_LBDV_Basis_at_Quad_Pts_Mats[:, :, :, 3] = (
+                self.SPH_Phi_Phi_Der_At_Quad_Pts
+            )
 
             with open(LBDV_Basis_at_Quad_Pts_Mats_filepath, "wb") as f_lbdv_basis:
                 pkl.dump(To_Pickle_LBDV_Basis_at_Quad_Pts_Mats, f_lbdv_basis)

diff --git a/src/napari_stress/_stress/manifold_SPB.py b/src/napari_stress/_stress/manifold_SPB.py
@@ -896,12 +896,8 @@ def __init__(
             + self.Z_theta_B_Pts * self.Z_phi_B_Pts
         )
 
-        self.G_A_pts = (
-            self.X_phi_A_Pts**2 + self.Y_phi_A_Pts**2 + self.Z_phi_A_Pts**2
-        )
-        self.G_B_pts = (
-            self.X_phi_B_Pts**2 + self.Y_phi_B_Pts**2 + self.Z_phi_B_Pts**2
-        )
+        self.G_A_pts = self.X_phi_A_Pts**2 + self.Y_phi_A_Pts**2 + self.Z_phi_A_Pts**2
+        self.G_B_pts = self.X_phi_B_Pts**2 + self.Y_phi_B_Pts**2 + self.Z_phi_B_Pts**2
 
         # |g| = (\sqrt|g|)^2
         self.Metric_Factor_Squared_A = self.E_A_pts * self.G_A_pts - self.F_A_pts**2

diff --git a/src/napari_stress/_utils/coordinate_conversion.py b/src/napari_stress/_utils/coordinate_conversion.py
@@ -114,9 +114,7 @@ def cartesian_to_elliptical(
 
         U_coors_calc[pt_numb] = U_pt
 
-        cylinder_r = np.sqrt(
-            yt_0**2 + yt_1**2
-        )  # r in cylinderical coors for y_tilde
+        cylinder_r = np.sqrt(yt_0**2 + yt_1**2)  # r in cylinderical coors for y_tilde
         cyl_r_exp = np.sqrt(
             (lengths[0] * np.cos(U_pt)) ** 2 + (lengths[1] * np.sin(U_pt)) ** 2
         )