Merge pull request #360 from Sai-Suraj-27/update_pre-commit

Updated the `.pre-commit-config.yaml` file.

.pre-commit-config.yaml

@@ -1,14 +1,19 @@
 # See https://pre-commit.com for more information
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+    rev: v3.3.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
     -   id: black
         args: ["--line-length", "120"] # Adjust the max line length value as needed.
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+    -   id: isort
+        args: ["--line-length", "120", "--profile", "black"]

examples/subgrids/cylinder_fs.py

@@ -10,6 +10,7 @@ source is used with a waveform shaped as the first derivative of a gaussian.
 """
 
 from pathlib import Path
+
 import gprMax
 from gprMax.materials import calculate_water_properties
 

gprMax/cmds_geometry/cmds_geometry.py

@@ -18,10 +18,11 @@
 
 import logging
 
-import gprMax.config as config
 import numpy as np
 from scipy.spatial.transform import Rotation as R
 
+import gprMax.config as config
+
 logger = logging.getLogger(__name__)
 
 

gprMax/cmds_geometry/fractal_box_builder.py

@@ -18,9 +18,10 @@
 
 import logging
 
-import gprMax.config as config
 import numpy as np
 
+import gprMax.config as config
+
 from ..cython.geometry_primitives import build_voxels_from_array, build_voxels_from_array_mask
 from .cmds_geometry import UserObjectGeometry
 

gprMax/cmds_geometry/geometry_objects_read.py

@@ -19,9 +19,10 @@
 import logging
 from pathlib import Path
 
-import gprMax.config as config
 import h5py
 
+import gprMax.config as config
+
 from ..cython.geometry_primitives import build_voxels_from_array
 from ..hash_cmds_file import get_user_objects
 from ..utilities.utilities import round_value

gprMax/cmds_singleuse.py

@@ -20,10 +20,11 @@ import inspect
 import logging
 from pathlib import Path
 
-import gprMax.config as config
 import numpy as np
 from scipy import interpolate
 
+import gprMax.config as config
+
 from .pml import PML
 from .utilities.host_info import set_omp_threads
 from .waveforms import Waveform

gprMax/config.pxd

@@ -17,8 +17,8 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-cimport numpy as np
 
+cimport numpy as np
 
 ctypedef fused float_or_double:
     float

gprMax/cuda_opencl/knl_fields_updates.py

@@ -223,7 +223,7 @@ update_electric_dispersive_A = {
     //                                              component arrays.
 
     $CUDA_IDX
-    
+
     // Convert the linear index to subscripts for 3D field arrays
     int x = i / ($NY_FIELDS * $NZ_FIELDS);
     int y = (i % ($NY_FIELDS * $NZ_FIELDS)) / $NZ_FIELDS;
@@ -335,7 +335,7 @@ update_electric_dispersive_B = {
     //                                              component arrays.
 
     $CUDA_IDX
-        
+
     // Convert the linear index to subscripts for 3D field arrays
     int x = i / ($NY_FIELDS * $NZ_FIELDS);
     int y = (i % ($NY_FIELDS * $NZ_FIELDS)) / $NZ_FIELDS;

gprMax/cuda_opencl/knl_snapshots.py

@@ -18,7 +18,6 @@
 
 from string import Template
 
-
 store_snapshot = {
     "args_cuda": Template(
         """

gprMax/cuda_opencl/knl_store_outputs.py

@@ -18,7 +18,6 @@
 
 from string import Template
 
-
 store_outputs = {
     "args_cuda": Template(
         """

gprMax/cython/geometry_primitives.pyx

@@ -17,20 +17,25 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
+
 cimport numpy as np
+
 np.seterr(divide='raise')
 from cython.parallel import prange
 
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_Ex
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_Ey
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_Ez
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_Hx
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_Hy
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_Hz
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_E
-from gprMax.cython.yee_cell_setget_rigid cimport unset_rigid_E
-from gprMax.cython.yee_cell_setget_rigid cimport set_rigid_H
-from gprMax.cython.yee_cell_setget_rigid cimport unset_rigid_H
+from gprMax.cython.yee_cell_setget_rigid cimport (
+    set_rigid_E,
+    set_rigid_Ex,
+    set_rigid_Ey,
+    set_rigid_Ez,
+    set_rigid_H,
+    set_rigid_Hx,
+    set_rigid_Hy,
+    set_rigid_Hz,
+    unset_rigid_E,
+    unset_rigid_H,
+)
+
 from gprMax.utilities.utilities import round_value
 
 

gprMax/cython/yee_cell_build.pyx

@@ -17,14 +17,18 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
+
 cimport numpy as np
 
-from gprMax.cython.yee_cell_setget_rigid cimport get_rigid_Ex
-from gprMax.cython.yee_cell_setget_rigid cimport get_rigid_Ey
-from gprMax.cython.yee_cell_setget_rigid cimport get_rigid_Ez
-from gprMax.cython.yee_cell_setget_rigid cimport get_rigid_Hx
-from gprMax.cython.yee_cell_setget_rigid cimport get_rigid_Hy
-from gprMax.cython.yee_cell_setget_rigid cimport get_rigid_Hz
+from gprMax.cython.yee_cell_setget_rigid cimport (
+    get_rigid_Ex,
+    get_rigid_Ey,
+    get_rigid_Ez,
+    get_rigid_Hx,
+    get_rigid_Hy,
+    get_rigid_Hz,
+)
+
 from gprMax.materials import Material
 
 

gprMax/materials.py

@@ -16,13 +16,12 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import numpy as np
 import logging
 
+import numpy as np
 
 import gprMax.config as config
 
-
 logger = logging.getLogger(__name__)
 
 

gprMax/receivers.py

@@ -16,9 +16,10 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import gprMax.config as config
 import numpy as np
 
+import gprMax.config as config
+
 
 class Rx:
     """Receiver output points."""

gprMax/snapshots.py

@@ -17,8 +17,8 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging
-from pathlib import Path
 import sys
+from pathlib import Path
 
 import h5py
 import numpy as np

gprMax/sources.py

@@ -18,9 +18,10 @@
 
 from copy import deepcopy
 
-import gprMax.config as config
 import numpy as np
 
+import gprMax.config as config
+
 from .fields_outputs import Ix, Iy, Iz
 from .utilities.utilities import round_value
 

gprMax/subgrids/precursor_nodes.py

@@ -17,6 +17,7 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging
+
 import numpy as np
 from scipy import interpolate
 

gprMax/user_inputs.py

@@ -18,9 +18,10 @@
 
 import logging
 
-import gprMax.config as config
 import numpy as np
 
+import gprMax.config as config
+
 from .subgrids.grid import SubGridBaseGrid
 from .utilities.utilities import round_value
 

gprMax/waveforms.py

@@ -17,6 +17,7 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging
+
 import numpy as np
 
 logger = logging.getLogger(__name__)

setup.py

@@ -29,7 +29,6 @@ from Cython.Build import cythonize
 from jinja2 import Environment, FileSystemLoader
 from setuptools import Extension, find_packages, setup
 
-
 # Check Python version
 MIN_PYTHON_VERSION = (3, 7)
 if sys.version_info[:2] < MIN_PYTHON_VERSION:

testing/analytical_solutions.py

@@ -24,7 +24,7 @@ from gprMax.waveforms import Waveform
 
 def hertzian_dipole_fs(iterations, dt, dxdydz, rx):
     """Analytical solution of a z-directed Hertzian dipole in free space with a
-        current waveform of the form of the first derivative of a Gaussian 
+        current waveform of the form of the first derivative of a Gaussian
         (http://dx.doi.org/10.1016/0021-9991(83)90103-1).
 
     Args:

testing/benchmarking/bench_simple.py

@@ -4,10 +4,10 @@
 """
 
 
-from pathlib import Path
-import gprMax
-
 import itertools
+from pathlib import Path
+
+import gprMax
 
 # File path for output
 fn = Path(__file__)

testing/models_pmls/pml_3D_pec_plate/pml_3D_pec_plate.py

@@ -1,8 +1,9 @@
 from pathlib import Path
 
-import gprMax
 import numpy as np
 
+import gprMax
+
 # File path for output
 fn = Path(__file__)
 parts = fn.parts

testing/models_pmls/pml_3D_pec_plate/pml_3D_pec_plate_ref.py

@@ -1,8 +1,9 @@
 from pathlib import Path
 
-import gprMax
 import numpy as np
 
+import gprMax
+
 # File path for output
 fn = Path(__file__)
 parts = fn.parts

testing/test_models.py

@@ -20,11 +20,11 @@ import logging
 import sys
 from pathlib import Path
 
-import gprMax
 import h5py
 import matplotlib.pyplot as plt
 import numpy as np
 
+import gprMax
 from testing.analytical_solutions import hertzian_dipole_fs
 
 logger = logging.getLogger(__name__)

toolboxes/AntennaPatterns/initial_save.py

@@ -9,11 +9,12 @@ import argparse
 import logging
 import os
 
-import gprMax.config as config
 import h5py
 import matplotlib.pyplot as plt
 import numpy as np
 
+import gprMax.config as config
+
 logger = logging.getLogger(__name__)
 
 

toolboxes/AntennaPatterns/plot_fields.py

@@ -9,10 +9,11 @@ import argparse
 import logging
 import os
 
-import gprMax.config as config
 import matplotlib.pyplot as plt
 import numpy as np
 
+import gprMax.config as config
+
 logger = logging.getLogger(__name__)
 
 

toolboxes/DebyeFit/Debye_Fit.py

@@ -14,7 +14,6 @@ import matplotlib.gridspec as gridspec
 import numpy as np
 import scipy.interpolate
 from matplotlib import pylab as plt
-
 from optimization import DA_DLS, DE_DLS, PSO_DLS
 
 

toolboxes/DebyeFit/examples/example_ColeCole.py

@@ -2,7 +2,8 @@
 # "Incorporating dispersive electrical properties in FDTD GPR models
 # using a general Cole-Cole dispersion function,"
 # 2012 14th International Conference on Ground Penetrating Radar (GPR), 2012, pp. 232-236
-import os, sys
+import os
+import sys
 
 sys.path.append(os.path.join(os.path.dirname(__file__), ".."))
 from Debye_Fit import HavriliakNegami

toolboxes/Plotting/plot_Ascan.py

@@ -24,6 +24,7 @@ import h5py
 import matplotlib.gridspec as gridspec
 import matplotlib.pyplot as plt
 import numpy as np
+
 from gprMax.receivers import Rx
 from gprMax.utilities.utilities import fft_power
 

toolboxes/Plotting/plot_source_wave.py

@@ -22,6 +22,7 @@ from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
+
 from gprMax.utilities.utilities import fft_power, round_value
 from gprMax.waveforms import Waveform
 

toolboxes/STLtoVoxel/convert.py

@@ -7,12 +7,12 @@ from . import slice
 def convert_meshes(meshes, discretization, parallel=True):
     scale, shift, shape = slice.calculate_scale_shift(meshes, discretization)
     vol = np.zeros(shape[::-1], dtype=np.int8)
-    vol.fill(-1) # Fill array with -1 to indicate background in gprMax
+    vol.fill(-1)  # Fill array with -1 to indicate background in gprMax
 
     for mesh_ind, org_mesh in enumerate(meshes):
         slice.scale_and_shift_mesh(org_mesh, scale, shift)
         cur_vol = slice.mesh_to_plane(org_mesh, shape, parallel)
-        vol[cur_vol] = mesh_ind # Removed plus 1 to work with gprMax material indexing
+        vol[cur_vol] = mesh_ind  # Removed plus 1 to work with gprMax material indexing
 
     return vol, scale, shift
 

toolboxes/STLtoVoxel/slice.py

@@ -3,9 +3,10 @@ import multiprocessing as mp
 import sys
 
 import numpy as np
-from gprMax.utilities.utilities import get_terminal_width
 from tqdm import tqdm
 
+from gprMax.utilities.utilities import get_terminal_width
+
 from . import perimeter
 
 

toolboxes/STLtoVoxel/stltovoxel.py

@@ -16,10 +16,10 @@ if __name__ == "__main__":
         description="Allows the user to convert a STL files to voxelized mesh.",
         usage="cd gprMax; python -m toolboxes.STLtoVoxel.stltovoxel stlfilename -matindex -dxdydz",
     )
-    parser.add_argument("stlfiles", help="can be the filename of a single STL file, or the path to folder containing multiple STL files")
     parser.add_argument(
-        "-dxdydz", type=float, required=True, help="discretisation to use in voxelisation process"
+        "stlfiles", help="can be the filename of a single STL file, or the path to folder containing multiple STL files"
     )
+    parser.add_argument("-dxdydz", type=float, required=True, help="discretisation to use in voxelisation process")
     args = parser.parse_args()
 
     if os.path.isdir(args.stlfiles):
@@ -52,4 +52,4 @@ if __name__ == "__main__":
     #     for i, file in enumerate(files):
     #         name = os.path.splitext(os.path.basename(file))[0]
     #         f.write(f"#material: {i + 1} 0 1 0 {name}" + "\n")
-    # logger.info(f"Written materials file: {filename_mats}")
+    # logger.info(f"Written materials file: {filename_mats}")