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

toolboxes/AustinManWoman/head_only_h5.py

@@ -8,22 +8,24 @@ logger = logging.getLogger(__name__)
 
 
 # Parse command line arguments
-parser = argparse.ArgumentParser(description='Writes a HDF5 file of AustinMan or AustinWoman head only.', usage='python head_only_hdf5 filename')
-parser.add_argument('filename', help='name and path to (HDF5) file containing AustinMan or AustinWoman model')
+parser = argparse.ArgumentParser(
+    description="Writes a HDF5 file of AustinMan or AustinWoman head only.", usage="python head_only_hdf5 filename"
+)
+parser.add_argument("filename", help="name and path to (HDF5) file containing AustinMan or AustinWoman model")
 args = parser.parse_args()
 
 # Read full body HDF5 file
-f = h5py.File(args.filename, 'r')
-dx_dy_dz = f.attrs['dx_dy_dz']
-data = f['/data'][:, :, :]
+f = h5py.File(args.filename, "r")
+dx_dy_dz = f.attrs["dx_dy_dz"]
+data = f["/data"][:, :, :]
 
 # Define head as last 1/8 of total body height
 nzhead = 7 * int(data.shape[2] / 8)
 
-logger.info(f'Dimensions of head model: {data.shape[0]:g} x {data.shape[1]:g} x {data.shape[2] - nzhead:g} cells')
+logger.info(f"Dimensions of head model: {data.shape[0]:g} x {data.shape[1]:g} x {data.shape[2] - nzhead:g} cells")
 
 # Write HDF5 file
-headfile = os.path.splitext(args.filename)[0] + '_head.h5'
-f = h5py.File(headfile, 'w')
-f.attrs['dx_dy_dz'] = dx_dy_dz
-f['/data'] = data[:, :, nzhead:data.shape[2]]
+headfile = os.path.splitext(args.filename)[0] + "_head.h5"
+f = h5py.File(headfile, "w")
+f.attrs["dx_dy_dz"] = dx_dy_dz
+f["/data"] = data[:, :, nzhead : data.shape[2]]