[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: configure|\.*.msh|\.*.rng|^h5hut/\.*|^libjudy\.*|^libmba2d\.*|^libmba3d\.*|^libspud\.*|^spatialindex-1.8.0\.*
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
     -   id: check-ast
     -   id: check-builtin-literals
@@ -20,20 +20,20 @@ repos:
         exclude: ref_vtk_hexahedra.vtu
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 25.1.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 6.0.0
     hooks:
     -   id: isort
         args: ["--profile", "black", "--filter-files"]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.6.0
+    rev: v3.19.1
     hooks:
     -   id: pyupgrade
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
     -   id: flake8
         args: ["--max-line-length", "88", "--extend-ignore", "E203,E722"]

mayavi/mayavi_amcg/filters/boundary_marker_editor.py

@@ -193,9 +193,9 @@ def perform_mask(self):
         # value is the new cell_id of the corresponding cell in the masked grid
         self._cell_mappings = list(
             map(
-                lambda masked, cell_id: None
-                if masked
-                else unmasked_cells_list.insert_next_id(cell_id),
+                lambda masked, cell_id: (
+                    None if masked else unmasked_cells_list.insert_next_id(cell_id)
+                ),
                 in_masked,
                 cell_ids,
             )

python/fluidity/ocean_biology.py

@@ -68,9 +68,7 @@ def pznd(state, parameters):
         G_P = (g * p_P * P_n**2 * Z_n) / (k**2 + p_P * P_n**2 + p_D * D_n**2)
 
         # Zooplankton grazing of detritus.
-        G_D = (g * (1 - p_P) * D_n**2 * Z_n) / (
-            k**2 + p_P * P_n**2 + p_D * D_n**2
-        )
+        G_D = (g * (1 - p_P) * D_n**2 * Z_n) / (k**2 + p_P * P_n**2 + p_D * D_n**2)
 
         # Death rate of phytoplankton.
         De_P = mu_P * P_n * P_n / (P_n + 0.2)
@@ -327,12 +325,7 @@ def six_component(state, parameters):
 
         # Chl growth scaling factor
         # R_P=(theta_m/theta)*J*(Q_N+Q_A)/(alpha*I_n+1e-7)
-        R_P = (
-            (theta_m / theta)
-            * (Q_N + Q_A)
-            * v
-            / (v**2 + alpha**2 * I_n**2) ** 0.5
-        )
+        R_P = (theta_m / theta) * (Q_N + Q_A) * v / (v**2 + alpha**2 * I_n**2) ** 0.5
 
         # Primary production
         X_P = J * (Q_N + Q_A) * P_n
@@ -350,9 +343,7 @@ def six_component(state, parameters):
         # G_D = (g * epsilon * (1 - p_P) * D_n**2 * Z_n) / (
         #     g + epsilon * (p_P * P_n**2 + p_D * D_n**2)
         # )
-        G_D = (g * (1 - p_P) * D_n**2 * Z_n) / (
-            epsilon + (p_P * P_n**2 + p_D * D_n**2)
-        )
+        G_D = (g * (1 - p_P) * D_n**2 * Z_n) / (epsilon + (p_P * P_n**2 + p_D * D_n**2))
 
         # Death rate of phytoplankton.
         # There is an additional linear term because we have a unified model

python/fluidity/state_types.py

@@ -145,6 +145,7 @@ def remap_ele(self, ele_number, mesh):
 
 class ScalarField(Field):
     "A scalar field"
+
     description = "ScalarField"
 
     def __init__(self, n, v, ft, op):
@@ -155,6 +156,7 @@ def __init__(self, n, v, ft, op):
 
 class VectorField(Field):
     "A vector field"
+
     description = "VectorField"
 
     def __init__(self, n, v, ft, op, dim):
@@ -166,6 +168,7 @@ def __init__(self, n, v, ft, op, dim):
 
 class TensorField(Field):
     "A tensor field"
+
     description = "VectorField"
 
     def __init__(self, n, v, ft, op, dim0, dim1):
@@ -337,6 +340,7 @@ def eval(self, x):
 
 class Transform:
     "Transform with information about the detwei and Jacobian"
+
     # Note that so far only the dim == ldim == (2||3) have been tested
 
     def __init__(self, ele_num, field):

tests/mphase_rogue_shock_tube_dense_bed_nylon/get_cloud_front.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 """
-   Python script to measure the position of the particle cloud front in
-   simulations of the shock tube experiment by Rogue et al. (1998).
-   Written by Christian Jacobs.
+Python script to measure the position of the particle cloud front in
+simulations of the shock tube experiment by Rogue et al. (1998).
+Written by Christian Jacobs.
 """
 
 import matplotlib.pyplot as plt

tests/netcdf_read_free_surface/height.py

@@ -6,8 +6,6 @@ def function(position):
     xg = 3.0 * position[0]
     yg = 3.0 * position[1]
     h1 = multivariate_normal.pdf([xg, yg], cov=[[1, 0], [0, 1]])
-    h2 = multivariate_normal.pdf(
-        [xg, yg], mean=[1, 1], cov=[[1.5**2, 0], [0, 0.5**2]]
-    )
+    h2 = multivariate_normal.pdf([xg, yg], mean=[1, 1], cov=[[1.5**2, 0], [0, 0.5**2]])
     h = 10.0 * (h1 - h2)
     return h

tests/square-convection/checkpoint/change_options

@@ -17,9 +17,9 @@ for i in range(len(flml_options) - 1):
     line = flml_options[i]
     if "<simulation_name>" in line:
         # Change the simulation name
-        flml_options[
-            i + 1
-        ] = '<string_value lines="1">square-convection-picked-up</string_value>\n'
+        flml_options[i + 1] = (
+            '<string_value lines="1">square-convection-picked-up</string_value>\n'
+        )
 
 for i in range(len(flml_options)):
     if "<checkpointing>" in flml_options[i]: