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

pre-commit-ci[bot] · pre-commit-ci[bot] · commit cd7aed52ac3b · 2023-06-13T08:03:11.000Z
for more information, see https://pre-commit.ci
diff --git a/examples/backward_facing_step_2d/postprocessor_2d.py b/examples/backward_facing_step_2d/postprocessor_2d.py
@@ -66,9 +66,9 @@ def sort_nicely(my_list):
 
 ###################################################################
 
+
 # Reattachment length:
 def reattachment_length(filelist):
-
     print("Calculating reattachment point locations using change of x-velocity sign\n")
 
     results = []
@@ -140,9 +140,9 @@ def reattachment_length(filelist):
 
 #########################################################################
 
+
 # Velocity profiles:
 def meanvelo(file, x, y):
-
     print("\nRunning velocity profile script on files at times...\n")
 
     # create array of points. Correct for origin not at step.
diff --git a/examples/backward_facing_step_3d/extract_data.py b/examples/backward_facing_step_3d/extract_data.py
@@ -83,7 +83,6 @@ def restresseslemoin(off):
 
 
 def velocityprofileslemoin():
-
     Le = open(str(mydir) + "/Le-profiles/Le-profile1-U-x4.dat").readlines()
     Le_u4 = [float(line.split()[0]) for line in Le]
     Le_y4 = [float(line.split()[1]) for line in Le]
@@ -130,7 +129,6 @@ def velocityprofileslemoin():
 
 
 def ercoftacvelocityprofiles():
-
     y4 = []
     U4 = []
     y6 = []
@@ -168,7 +166,6 @@ def ercoftacvelocityprofiles():
 
 
 def ercoftacrestressprofiles():
-
     datafile = open(str(mydir) + "/Ercoftac-test31-BFS/BFS-SEM-ERCOFTAC181-table.dat")
     print("reading in data from file: BFS-SEM-ERCOFTAC181-table.dat")
     # ignore header line
@@ -191,7 +188,6 @@ def ercoftacrestressprofiles():
 
 
 def panjwaniprofiles(variable):
-
     off = 0.05 if variable == "uu" else 0.0
     inv = -1.0 if variable == "uv" else 1.0
     # get data from relevant files
diff --git a/examples/backward_facing_step_3d/postprocessor_3d.py b/examples/backward_facing_step_3d/postprocessor_3d.py
@@ -69,6 +69,7 @@ def sort_nicely(my_list):
 
 ###################################################################
 
+
 # Reattachment length:
 def reatt_length(filelist, zarray):
     print("Calculating reattachment point locations using change of x-velocity sign\n")
@@ -155,6 +156,7 @@ def reatt_length(filelist, zarray):
 
 #########################################################################
 
+
 # Velocity profiles:
 def velo(filelist, xarray, zarray, yarray):
     print("\nRunning mean velocity profile script on files at times...\n")
diff --git a/examples/lock_exchange/plot_data.py b/examples/lock_exchange/plot_data.py
@@ -182,7 +182,6 @@ def Froudenumber(flmlname):
 
 
 def mixing(flmlname):
-
     print("\n********** Calculating the mixing diagnostics\n")
     # warn user about assumptions
     print(
diff --git a/python/elementtree/ElementPath.py b/python/elementtree/ElementPath.py
@@ -62,7 +62,6 @@ class xpath_descendant_or_self:
 
 
 class Path:
-
     ##
     # Create an Path instance from an XPath expression.
 
diff --git a/python/fluidity_ufl/ufl_fortran.py b/python/fluidity_ufl/ufl_fortran.py
@@ -40,7 +40,6 @@ def __init__(self, integral, dim="dim"):
         self.map_sum_indices()
 
     def fortran(self):
-
         dim_indices = ["dim" + str(i) + "_i" for i in range(self.integral.rank)]
 
         name, declaration, lhs = self.function_spec(dim_indices)
@@ -149,7 +148,6 @@ def iterfunctions(self):
             yield self.integral.trial
 
     def function_spec(self, dim_indices):
-
         name = "integral"
         declaration = "real, dimension("
         lhs_args = dim_indices + ["test_i"]
@@ -160,11 +158,9 @@ def function_spec(self, dim_indices):
             for i in f.indices:
                 # Slices are free indices.
                 if isinstance(i, slice):
-
                     declaration = declaration + str(self.dim) + ", "
 
                 else:
-
                     name = name + "_i" + str(self.sum_index_map[i.id])
 
         name = name + "_" + self.integral.measure.name
@@ -201,7 +197,6 @@ def set_arguments(self):
         self.actual_arguments = []
 
         for f in self.iterfunctions():
-
             args = function_to_arguments(f)
             self.dummy_arguments.append(args[0])
             self.actual_arguments.append(args[1])
@@ -238,12 +233,10 @@ def function_to_arguments(function):
 
 
 def indent(code):
-
     return ["  " + line for line in code]
 
 
 def do_loop(var, size, body):
-
     code = ["do " + var + " = 1, " + str(size)] + indent(body) + ["end do"]
 
     return code
diff --git a/tests/biology_conservation/values_per_node.py b/tests/biology_conservation/values_per_node.py
@@ -2,7 +2,6 @@
 
 
 def values_per_node(file):
-
     u = vtktools.vtu(file)
     zoo = u.GetScalarField("Zooplankton")
     phyto = u.GetScalarField("Phytoplankton")
diff --git a/tests/netcdf_read_errors/createnetcdf.py b/tests/netcdf_read_errors/createnetcdf.py
@@ -16,7 +16,6 @@ def create(
     incorrectdimension=False,
     incorrectvariable=False,
 ):
-
     if missingdata:
         filename = "missingdata.nc"
         description = ", with missing data."
diff --git a/tests/turbine_flux_dg_2d/mesh/scripts/triangle.py b/tests/turbine_flux_dg_2d/mesh/scripts/triangle.py
@@ -137,7 +137,6 @@ def pnode(fnode):
     nbnodes = 0
 
     for line in fnode:
-
         if line[0] == "#":
             continue
         else:
@@ -220,7 +219,6 @@ def peles(fele):
     count = 0
     nbeles = 0
     for line in fele:
-
         if line[0] == "#":
             continue
         else:
diff --git a/tests/turbine_flux_dg_2plus1/mesh/scripts/triangle.py b/tests/turbine_flux_dg_2plus1/mesh/scripts/triangle.py
@@ -137,7 +137,6 @@ def pnode(fnode):
     nbnodes = 0
 
     for line in fnode:
-
         if line[0] == "#":
             continue
         else:
@@ -220,7 +219,6 @@ def peles(fele):
     count = 0
     nbeles = 0
     for line in fele:
-
         if line[0] == "#":
             continue
         else:
diff --git a/tests/turbine_flux_penalty_2d/mesh/scripts/triangle.py b/tests/turbine_flux_penalty_2d/mesh/scripts/triangle.py
@@ -137,7 +137,6 @@ def pnode(fnode):
     nbnodes = 0
 
     for line in fnode:
-
         if line[0] == "#":
             continue
         else:
@@ -220,7 +219,6 @@ def peles(fele):
     count = 0
     nbeles = 0
     for line in fele:
-
         if line[0] == "#":
             continue
         else:
diff --git a/tests/turbine_flux_penalty_2plus1/mesh/scripts/triangle.py b/tests/turbine_flux_penalty_2plus1/mesh/scripts/triangle.py
@@ -137,7 +137,6 @@ def pnode(fnode):
     nbnodes = 0
 
     for line in fnode:
-
         if line[0] == "#":
             continue
         else:
@@ -220,7 +219,6 @@ def peles(fele):
     count = 0
     nbeles = 0
     for line in fele:
-
         if line[0] == "#":
             continue
         else:
diff --git a/tests/wetting_and_drying_balzano1_cg/plotfs_detec.py b/tests/wetting_and_drying_balzano1_cg/plotfs_detec.py
@@ -27,7 +27,6 @@ def bathymetry_function(X):
 
 # Main #
 def main(argv=None):
-
     filename = ""
     timestep_ana = 0.0
     dzero = 0.01
diff --git a/tools/clean_mayavi_mesh.py b/tools/clean_mayavi_mesh.py
@@ -43,11 +43,9 @@ def find_bounding_box(ps, margin=10):
 
 
 def set_bounding_box(ps, margin):
-
     bb = find_bounding_box(ps, margin)
 
     for i in range(len(ps)):
-
         if bb_re.match(ps[i]):
             ps[i] = "%%BoundingBox: " + " ".join(map(str, bb)) + "\n"
 
@@ -58,9 +56,7 @@ def set_bounding_box(ps, margin):
 
 
 def set_linestyle(ps):
-
     for i in range(len(ps)):
-
         if linestyle_re.match(ps[i]):
             ps[i] = "1 setlinecap 1 setlinejoin\n"
             return
@@ -69,7 +65,6 @@ def set_linestyle(ps):
 
 
 def process_file(inname, outname, options):
-
     ps = open(inname).readlines()
 
     set_bounding_box(ps, options.margin)
diff --git a/tools/edge_length_distribution.py b/tools/edge_length_distribution.py
@@ -95,8 +95,8 @@ def pair_off(nodes):
     # e.g. for [1,5,7,9] will yield [1,5], [1,7], [1,9]
     # then knock off 1 and yield [5,7], [5,9]
     # then knock off 5 and yield [7,9]
-    for (idx_i, node) in enumerate(nodes):
-        for (idx_j, node_j) in enumerate(nodes[idx_i + 1 :]):
+    for idx_i, node in enumerate(nodes):
+        for idx_j, node_j in enumerate(nodes[idx_i + 1 :]):
             yield (node, node_j)
 
 
@@ -119,7 +119,6 @@ def key(s):
 
 
 def GetEdgeLengths(data):
-
     eles = data.ugrid.GetNumberOfCells()
     edgeset = set()
 
@@ -145,7 +144,6 @@ def GetEdgeLengths(data):
 
 
 def PlotEdgeLengths(edge_lengths_all, time, options):
-
     for i in range(len(edge_lengths_all)):
         plt.figure(num=None, figsize=(16.5, 11.5))
         plt.hist(edge_lengths_all[i], options.no_bins)
@@ -166,7 +164,6 @@ def PlotEdgeLengths(edge_lengths_all, time, options):
 
 
 def PlotMaxMin(edge_lengths_all, time):
-
     min_edgelength = []
     max_edgelength = []
 
@@ -195,7 +192,6 @@ def PlotMaxMin(edge_lengths_all, time):
 
 
 def PlotCumulative(edge_lengths_all, options):
-
     all_vals = []
     for edge_lengths in edge_lengths_all:
         all_vals = all_vals + edge_lengths
@@ -235,7 +231,6 @@ def PlotCumulative(edge_lengths_all, options):
     pass
 
 if options.plot_only is True:
-
     try:
         time_log = open("edge_length_distribution_plots/time.log")
     except OSError:
@@ -264,7 +259,6 @@ def PlotCumulative(edge_lengths_all, options):
         edge_lengths_all.append(line)
 
 else:
-
     time_log = open("edge_length_distribution_plots/time.log", "w")
     edge_lengths_log = open("edge_length_distribution_plots/edge_lengths.log", "w")
     if options.end_vtu is None:
diff --git a/tools/make_check_options.py b/tools/make_check_options.py
@@ -44,13 +44,11 @@ def safe_decode(x):
 module_list = []
 
 for filename in fortran_files:
-
     fortran = open(filename, "rb").read().decode("utf-8")
 
     modules = module_re.findall(fortran)
 
     for module in modules:
-
         if re.search(
             r"^\s*subroutine\s+" + module + r"_check_options\S*\s*$",
             fortran,
@@ -59,7 +57,6 @@ def safe_decode(x):
             module_list.append(module)
 
 for module in module_list:
-
     output.write(
         safe_decode("  use " + module + ", only: " + module + "_check_options\n")
     )
@@ -74,7 +71,6 @@ def safe_decode(x):
 )
 
 for module in module_list:
-
     output.write(safe_decode("  call " + module + "_check_options\n"))
 
 output.write(safe_decode(footer))
diff --git a/tools/make_register_diagnostics.py b/tools/make_register_diagnostics.py
@@ -44,13 +44,11 @@ def safe_decode(x):
 module_list = []
 
 for filename in fortran_files:
-
     fortran = open(filename, "rb").read().decode("utf-8")
 
     modules = module_re.findall(fortran)
 
     for module in modules:
-
         if re.search(
             r"^\s*subroutine\s+" + module + r"_register_diagnostic\s*$",
             fortran,
@@ -59,7 +57,6 @@ def safe_decode(x):
             module_list.append(module)
 
 for module in module_list:
-
     output.write(
         safe_decode("  use " + module + ", only: " + module + "_register_diagnostic\n")
     )
@@ -74,7 +71,6 @@ def safe_decode(x):
 )
 
 for module in module_list:
-
     output.write(safe_decode("  call " + module + "_register_diagnostic\n"))
 
 output.write(safe_decode(footer))
diff --git a/tools/profiling-graph.py b/tools/profiling-graph.py
@@ -40,7 +40,6 @@ def draw_graph(times, output):
 
 
 if __name__ == "__main__":
-
     import optparse
 
     usage = "usage: %prog [--subroutines] [--output] profiling-logs"
diff --git a/tools/rename_checkpoint.py b/tools/rename_checkpoint.py
