Install and run pre-commit

.pre-commit-config.yaml

@@ -1,4 +1,5 @@
 # See https://pre-commit.com for more information
+exclude: '\S*.map'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0

.readthedocs.yaml

@@ -24,5 +24,3 @@ python:
 
 sphinx:
    configuration: docs/source/conf.py
-
-

gprMax/fractals.py

@@ -56,7 +56,7 @@ class FractalSurface:
         self.nz = zf - zs
         self.dtype = np.dtype(np.complex128)
         self.seed = seed
-        self.dimension = dimension # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
+        self.dimension = dimension  # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
         self.weighting = np.array([1, 1], dtype=np.float64)
         self.fractalrange = (0, 0)
         self.filldepth = 0
@@ -157,7 +157,7 @@ class FractalVolume:
         self.averaging = False
         self.dtype = np.dtype(np.complex128)
         self.seed = seed
-        self.dimension = dimension # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
+        self.dimension = dimension  # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
         self.weighting = np.array([1, 1, 1], dtype=np.float64)
         self.nbins = 0
         self.fractalsurfaces = []

requirements.txt

@@ -14,6 +14,7 @@ scipy
 humanize
 # mpi4py
 numpy-stl
+pre-commit
 # pycuda
 # pyopencl
 terminaltables

testing/test_models.py

@@ -19,16 +19,15 @@
 import logging
 import sys
 from pathlib import Path
-from colorama import Fore, Style
 
 import h5py
 import matplotlib.pyplot as plt
 import numpy as np
+from colorama import Fore, Style
 
 import gprMax
-from testing.analytical_solutions import hertzian_dipole_fs
-
 from gprMax.utilities.logging import logging_config
+from testing.analytical_solutions import hertzian_dipole_fs
 
 logger = logging.getLogger(__name__)
 logging_config(name=__name__)

tests/.gitignore

@@ -5,4 +5,4 @@ reframe.log
 reframe.out
 reframe_perf.out
 
-configuration/user_config.py
+configuration/user_config.py

tests/job_scripts/archer2_map_single_node.slurm

@@ -21,4 +21,4 @@ mkdir -p profile/archer2/
 
 map -o="profile/archer2/gprMax_${1}d_${SLURM_CPUS_PER_TASK}t_$(date +%F_%H-%M)" --mpi=slurm --mpiargs="--hint=nomultithread --distribution=block:block" --profile python -m gprMax --log-level 25 src/benchmark_model_$1.in
 
-sacct --format=JobID,State,Submit,Start,End,Elapsed,NodeList --units=M -j $SLURM_JOBID
+sacct --format=JobID,State,Submit,Start,End,Elapsed,NodeList --units=M -j $SLURM_JOBID

tests/job_scripts/archer2_tests.slurm

@@ -14,4 +14,4 @@ source ../.venv/bin/activate
 
 reframe -C configuration/archer2_settings.py -c . -r --performance-report
 
-sacct --format=JobID,State,Submit,Start,End,Elapsed,NodeList --units=M -j $SLURM_JOBID
+sacct --format=JobID,State,Submit,Start,End,Elapsed,NodeList --units=M -j $SLURM_JOBID

tests/utilities/data.py

@@ -50,4 +50,4 @@ def calculate_diffs(test_data, ref_data):
         # Replace any NaNs or Infs from zero division
         diffs[:, i][np.invert(np.isfinite(diffs[:, i]))] = 0
 
-    return diffs
+    return diffs

tests/utilities/plotting.py

@@ -1,5 +1,5 @@
-from matplotlib import pyplot as plt
 import numpy as np
+from matplotlib import pyplot as plt
 
 
 def _plot_data(subplots, time, data, label=None, colour="r", line_style="-"):
@@ -46,8 +46,8 @@ def plot_diffs(time, diffs, plot_min=-160):
     """Plots ...
 
     Args:
-        time: 
+        time:
-        diffs: 
+        diffs:
         plot_min: minimum value of difference to plot (dB). Default: -160
 
     Returns:
@@ -82,4 +82,4 @@ def plot_diffs(time, diffs, plot_min=-160):
         ax.set_ylim(plot_min, y_max)
         ax.grid()
 
-    return fig
+    return fig

toolboxes/Utilities/outputfiles_merge.py

@@ -71,7 +71,7 @@ def get_output_data(filename, rxnumber, rxcomponent):
     return outputdata, dt
 
 
-def merge_files(outputfiles,  merged_outputfile=None, removefiles=False):
+def merge_files(outputfiles, merged_outputfile=None, removefiles=False):
     """Merges traces (A-scans) from multiple output files into one new file,
         then optionally removes the series of output files.
 
@@ -138,7 +138,9 @@ if __name__ == "__main__":
         usage="cd gprMax; python -m tools.outputfiles_merge basefilename",
     )
     parser.add_argument("basefilename", help="base name of output file series including path")
-    parser.add_argument("-o", "--output-file", default=None, type=str, required=False, help="location to save merged file")
+    parser.add_argument(
+        "-o", "--output-file", default=None, type=str, required=False, help="location to save merged file"
+    )
     parser.add_argument(
         "--remove-files", action="store_true", default=False, help="flag to remove individual output files after merge"
     )