Added a pre-commit config file and reformatted all the files accordingly by using it.

testing/test_experimental.py

@@ -26,80 +26,85 @@ import numpy as np
 
 logger = logging.getLogger(__name__)
 
-"""Plots a comparison of fields between given simulation output and experimental 
+"""Plots a comparison of fields between given simulation output and experimental
     data files.
 """
 
 # Parse command line arguments
-parser = argparse.ArgumentParser(description='Plots a comparison of fields between ' +
-                                    'given simulation output and experimental data files.', 
-                                 usage='cd gprMax; python -m testing.test_experimental modelfile realfile output')
-parser.add_argument('modelfile', help='name of model output file including path')
-parser.add_argument('realfile', help='name of file containing experimental data including path')
-parser.add_argument('output', help='output to be plotted, i.e. Ex Ey Ez', nargs='+')
+parser = argparse.ArgumentParser(
+    description="Plots a comparison of fields between " + "given simulation output and experimental data files.",
+    usage="cd gprMax; python -m testing.test_experimental modelfile realfile output",
+)
+parser.add_argument("modelfile", help="name of model output file including path")
+parser.add_argument("realfile", help="name of file containing experimental data including path")
+parser.add_argument("output", help="output to be plotted, i.e. Ex Ey Ez", nargs="+")
 args = parser.parse_args()
 
 modelfile = Path(args.modelfile)
 realfile = Path(args.realfile)
 
 # Model results
-f = h5py.File(Path(modelfile), 'r')
-path = '/rxs/rx1/'
+f = h5py.File(Path(modelfile), "r")
+path = "/rxs/rx1/"
 availablecomponents = list(f[path].keys())
 
 # Check for polarity of output and if requested output is in file
-if args.output[0][0] == 'm':
+if args.output[0][0] == "m":
     polarity = -1
     args.outputs[0] = args.output[0][1:]
 else:
     polarity = 1
 
 if args.output[0] not in availablecomponents:
-    logger.exception(f"{args.output[0]} output requested to plot, but the " +
-                     f"available output for receiver 1 is {', '.join(availablecomponents)}")
+    logger.exception(
+        f"{args.output[0]} output requested to plot, but the "
+        + f"available output for receiver 1 is {', '.join(availablecomponents)}"
+    )
     raise ValueError
 
 floattype = f[path + args.output[0]].dtype
-iterations = f.attrs['Iterations']
-dt = f.attrs['dt']
+iterations = f.attrs["Iterations"]
+dt = f.attrs["dt"]
 model = np.zeros(iterations, dtype=floattype)
 model = f[path + args.output[0]][:] * polarity
 model /= np.amax(np.abs(model))
 timemodel = np.linspace(0, 1, iterations)
-timemodel *= (iterations * dt)
+timemodel *= iterations * dt
 f.close()
 
 # Find location of maximum value from model
 modelmax = np.where(np.abs(model) == 1)[0][0]
 
 # Real results
-with open(realfile, 'r') as f:
+with open(realfile, "r") as f:
     real = np.loadtxt(f)
 real[:, 1] = real[:, 1] / np.amax(np.abs(real[:, 1]))
 realmax = np.where(np.abs(real[:, 1]) == 1)[0][0]
 
-difftime = - (timemodel[modelmax] - real[realmax, 0])
+difftime = -(timemodel[modelmax] - real[realmax, 0])
 
 # Plot modelled and real data
-fig, ax = plt.subplots(num=f'{modelfile.stem}_vs_{realfile.stem}',
-                       figsize=(20, 10),
-                       facecolor='w',
-                       edgecolor='w',)
-ax.plot(timemodel + difftime, model, 'r', lw=2, label='Model')
-ax.plot(real[:, 0], real[:, 1], 'r', ls='--', lw=2, label='Experiment')
-ax.set_xlabel('Time [s]')
-ax.set_ylabel('Amplitude')
+fig, ax = plt.subplots(
+    num=f"{modelfile.stem}_vs_{realfile.stem}",
+    figsize=(20, 10),
+    facecolor="w",
+    edgecolor="w",
+)
+ax.plot(timemodel + difftime, model, "r", lw=2, label="Model")
+ax.plot(real[:, 0], real[:, 1], "r", ls="--", lw=2, label="Experiment")
+ax.set_xlabel("Time [s]")
+ax.set_ylabel("Amplitude")
 ax.set_xlim([0, timemodel[-1]])
 # ax.set_ylim([-1, 1])
 ax.legend()
 ax.grid()
 
 # Save a PDF/PNG of the figure
-savename = f'{modelfile.stem}_vs_{realfile.stem}'
+savename = f"{modelfile.stem}_vs_{realfile.stem}"
 savename = modelfile.parent / savename
-# fig.savefig(savename.with_suffix('.pdf'), dpi=None, format='pdf', 
+# fig.savefig(savename.with_suffix('.pdf'), dpi=None, format='pdf',
 #             bbox_inches='tight', pad_inches=0.1)
-# fig.savefig(savename.with_suffix('.png'), dpi=150, format='png', 
+# fig.savefig(savename.with_suffix('.png'), dpi=150, format='png',
 #             bbox_inches='tight', pad_inches=0.1)
 
 plt.show()