CI: Pre-Commit isort (#242)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Maxence Thevenet <[email protected]>

.pre-commit-config.yaml

@@ -71,12 +71,12 @@ repos:
 
 # Sorts Python imports according to PEP8
 # https://www.python.org/dev/peps/pep-0008/#imports
-#- repo: https://github.com/pycqa/isort
-#  rev: 5.12.0
-#  hooks:
-#  - id: isort
-#    name: isort (python)
-#    args: ['--profile black']
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+    name: isort (python)
+    args: ["--profile", "black", "--filter-files"]
 
 # Python: Flake8 (checks only, does this support auto-fixes?)
 #- repo: https://github.com/PyCQA/flake8

docs/source/conf.py

@@ -13,6 +13,7 @@
 import os
 import sys
 from datetime import date
+
 from lasy import __version__
 
 sys.path.insert(0, os.path.abspath("../.."))

examples/example_gerchberg_saxton_algo.py

@@ -1,12 +1,13 @@
-from lasy.profiles.gaussian_profile import GaussianProfile
-from lasy.laser import Laser
-from lasy.utils.phase_retrieval import gerchberg_saxton_algo
+import copy
+
 import matplotlib.pyplot as plt
 import numpy as np
-from lasy.utils.zernike import zernike
-import copy
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 
+from lasy.laser import Laser
+from lasy.profiles.gaussian_profile import GaussianProfile
+from lasy.utils.phase_retrieval import gerchberg_saxton_algo
+from lasy.utils.zernike import zernike
 
 # DEFINE PHYSICAL PARAMETERS & CREATE LASER PROFILE
 wavelength = 800e-9

examples/example_modal_decomposition_data.py

@@ -1,20 +1,18 @@
+import matplotlib.pyplot as plt
 import numpy as np
+import skimage
+from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-from lasy.profiles.transverse.transverse_profile_from_data import (
-    TransverseProfileFromData,
-)
+from lasy.profiles.combined_profile import CombinedLongitudinalTransverseProfile
+from lasy.profiles.longitudinal.gaussian_profile import GaussianLongitudinalProfile
 from lasy.profiles.transverse.hermite_gaussian_profile import (
     HermiteGaussianTransverseProfile,
 )
-from lasy.profiles.longitudinal.gaussian_profile import GaussianLongitudinalProfile
-from lasy.profiles.combined_profile import CombinedLongitudinalTransverseProfile
+from lasy.profiles.transverse.transverse_profile_from_data import (
+    TransverseProfileFromData,
+)
 from lasy.utils.mode_decomposition import hermite_gauss_decomposition
 
-import matplotlib.pyplot as plt
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-import skimage
-
-
 # Define the transverse profile of the laser pulse
 img_url = "https://user-images.githubusercontent.com/27694869/228038930-d6ab03b1-a726-4b41-a378-5f4a83dc3778.png"
 intensityData = skimage.io.imread(img_url)

lasy/laser.py

@@ -1,7 +1,6 @@
 import numpy as np
-from scipy.constants import c
-
 from axiprop.lib import PropagatorFFT2, PropagatorResampling
+from scipy.constants import c
 
 from lasy.utils.grid import Grid
 from lasy.utils.laser_utils import (

lasy/optical_elements/parabolic_mirror.py

@@ -1,7 +1,8 @@
-from .optical_element import OpticalElement
 import numpy as np
 from scipy.constants import c
 
+from .optical_element import OpticalElement
+
 
 class ParabolicMirror(OpticalElement):
     r"""

lasy/profiles/__init__.py

@@ -1,8 +1,8 @@
 from .combined_profile import CombinedLongitudinalTransverseProfile
-from .gaussian_profile import GaussianProfile
 from .from_array_profile import FromArrayProfile
-from .from_openpmd_profile import FromOpenPMDProfile
 from .from_insight_file import FromInsightFile
+from .from_openpmd_profile import FromOpenPMDProfile
+from .gaussian_profile import GaussianProfile
 from .speckle_profile import SpeckleProfile
 
 __all__ = [

lasy/profiles/from_array_profile.py

@@ -1,5 +1,6 @@
-from scipy.interpolate import RegularGridInterpolator
 import numpy as np
+from scipy.interpolate import RegularGridInterpolator
+
 from .profile import Profile
 
 

lasy/profiles/from_insight_file.py

@@ -1,6 +1,7 @@
-import numpy as np
 import h5py
+import numpy as np
 from scipy.constants import c
+
 from .from_array_profile import FromArrayProfile
 
 

lasy/profiles/from_openpmd_profile.py

@@ -1,11 +1,13 @@
 import numpy as np
-from scipy.constants import c
 import openpmd_api as io
 from openpmd_viewer import OpenPMDTimeSeries
-from .from_array_profile import FromArrayProfile
-from lasy.utils.laser_utils import field_to_envelope, create_grid
+from scipy.constants import c
+
+from lasy.utils.laser_utils import create_grid, field_to_envelope
 from lasy.utils.openpmd_input import reorder_array
 
+from .from_array_profile import FromArrayProfile
+
 
 class FromOpenPMDProfile(FromArrayProfile):
     r"""

lasy/profiles/longitudinal/__init__.py

@@ -1,8 +1,8 @@
 from .cosine_profile import CosineLongitudinalProfile
 from .gaussian_profile import GaussianLongitudinalProfile
-from .super_gaussian_profile import SuperGaussianLongitudinalProfile
-from .longitudinal_profile_from_data import LongitudinalProfileFromData
 from .longitudinal_profile import LongitudinalProfile
+from .longitudinal_profile_from_data import LongitudinalProfileFromData
+from .super_gaussian_profile import SuperGaussianLongitudinalProfile
 
 __all__ = [
     "CosineLongitudinalProfile",

lasy/profiles/transverse/__init__.py

@@ -1,14 +1,14 @@
 from .gaussian_profile import GaussianTransverseProfile
 from .hermite_gaussian_profile import HermiteGaussianTransverseProfile
+from .jinc_profile import JincTransverseProfile
 from .laguerre_gaussian_profile import LaguerreGaussianTransverseProfile
 from .super_gaussian_profile import SuperGaussianTransverseProfile
-from .jinc_profile import JincTransverseProfile
-from .transverse_profile_from_data import TransverseProfileFromData
 from .transverse_profile import (
-    TransverseProfile,
-    SummedTransverseProfile,
     ScaledTransverseProfile,
+    SummedTransverseProfile,
+    TransverseProfile,
 )
+from .transverse_profile_from_data import TransverseProfileFromData
 
 __all__ = [
     "GaussianTransverseProfile",

lasy/profiles/transverse/hermite_gaussian_profile.py

@@ -1,6 +1,7 @@
+from math import factorial
+
 import numpy as np
 from scipy.special import hermite
-from math import factorial
 
 from .transverse_profile import TransverseProfile
 

lasy/profiles/transverse/jinc_profile.py

@@ -1,5 +1,6 @@
 import numpy as np
 import scipy.special as scispe
+
 from .transverse_profile import TransverseProfile
 
 

lasy/profiles/transverse/transverse_profile_from_data.py

@@ -1,6 +1,8 @@
 import numpy as np
 from scipy.interpolate import RegularGridInterpolator
+
 from lasy.utils.exp_data_utils import find_center_of_mass
+
 from .transverse_profile import TransverseProfile
 
 

lasy/utils/laser_utils.py

@@ -1,9 +1,10 @@
 import numpy as np
-from scipy.constants import c, epsilon_0, e, m_e
+from axiprop.containers import ScalarFieldEnvelope
+from axiprop.lib import PropagatorFFT2, PropagatorResampling
+from scipy.constants import c, e, epsilon_0, m_e
 from scipy.interpolate import interp1d
 from scipy.signal import hilbert
-from axiprop.lib import PropagatorFFT2, PropagatorResampling
-from axiprop.containers import ScalarFieldEnvelope
+
 from .grid import Grid
 
 

lasy/utils/mode_decomposition.py

@@ -1,15 +1,16 @@
+import math
+
+import numpy as np
+
+from lasy.profiles.transverse.hermite_gaussian_profile import (
+    HermiteGaussianTransverseProfile,
+)
 from lasy.profiles.transverse.transverse_profile import TransverseProfile
 from lasy.profiles.transverse.transverse_profile_from_data import (
     TransverseProfileFromData,
 )
-from lasy.profiles.transverse.hermite_gaussian_profile import (
-    HermiteGaussianTransverseProfile,
-)
 from lasy.utils.exp_data_utils import find_d4sigma
 
-import numpy as np
-import math
-
 
 def hermite_gauss_decomposition(laserProfile, n_x_max=12, n_y_max=12, res=1e-6):
     """

lasy/utils/openpmd_output.py

@@ -1,9 +1,11 @@
 import numpy as np
 import openpmd_api as io
 from scipy.constants import c
-from .laser_utils import field_to_vector_potential
+
 from lasy import __version__ as lasy_version
 
+from .laser_utils import field_to_vector_potential
+
 
 def write_to_openpmd_file(
     dim, file_prefix, file_format, grid, wavelength, pol, save_as_vector_potential=False

lasy/utils/phase_retrieval.py

@@ -1,4 +1,5 @@
 import copy
+
 import numpy as np
 
 

lasy/utils/zernike.py

@@ -1,6 +1,7 @@
-import numpy as np
 import math
 
+import numpy as np
+
 
 def get_zernike_nm(j):
     """

setup.py

@@ -1,4 +1,5 @@
 from setuptools import find_packages, setup
+
 import lasy  # In order to extract the version number
 
 # README file is long description

tests/test_gaussian_propagator.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 
+import numpy as np
 import pytest
 
-import numpy as np
 from lasy.laser import Laser
 from lasy.profiles.gaussian_profile import GaussianProfile
 

tests/test_gsalgo.py

@@ -1,13 +1,14 @@
 # -*- coding: utf-8 -*-
 
-import pytest
+import copy
 
 import numpy as np
+import pytest
+
 from lasy.laser import Laser
 from lasy.profiles.gaussian_profile import GaussianProfile
-from lasy.utils.zernike import zernike
 from lasy.utils.phase_retrieval import gerchberg_saxton_algo
-import copy
+from lasy.utils.zernike import zernike
 
 w0 = 25.0e-6  # m
 

tests/test_laser_profiles.py

@@ -1,27 +1,27 @@
 # -*- coding: utf-8 -*-
 
-import pytest
 import numpy as np
+import pytest
 from scipy.constants import c
 
 from lasy.laser import Laser
-from lasy.profiles.profile import Profile, SummedProfile, ScaledProfile
-from lasy.profiles import GaussianProfile, FromArrayProfile, SpeckleProfile
+from lasy.profiles import FromArrayProfile, GaussianProfile, SpeckleProfile
 from lasy.profiles.longitudinal import (
+    CosineLongitudinalProfile,
     GaussianLongitudinalProfile,
     SuperGaussianLongitudinalProfile,
-    CosineLongitudinalProfile,
 )
+from lasy.profiles.profile import Profile, ScaledProfile, SummedProfile
 from lasy.profiles.transverse import (
     GaussianTransverseProfile,
-    LaguerreGaussianTransverseProfile,
-    SuperGaussianTransverseProfile,
     HermiteGaussianTransverseProfile,
     JincTransverseProfile,
-    TransverseProfileFromData,
-    TransverseProfile,
-    SummedTransverseProfile,
+    LaguerreGaussianTransverseProfile,
     ScaledTransverseProfile,
+    SummedTransverseProfile,
+    SuperGaussianTransverseProfile,
+    TransverseProfile,
+    TransverseProfileFromData,
 )
 from lasy.utils.exp_data_utils import find_center_of_mass
 

tests/test_laser_utils.py

@@ -2,7 +2,7 @@
 
 from lasy.laser import Laser
 from lasy.profiles.gaussian_profile import GaussianProfile
-from lasy.utils.laser_utils import get_spectrum, compute_laser_energy, get_duration
+from lasy.utils.laser_utils import compute_laser_energy, get_duration, get_spectrum
 
 
 def get_gaussian_profile():

tests/test_parabolic_mirror.py

@@ -8,9 +8,10 @@
 """
 
 import numpy as np
+
 from lasy.laser import Laser
-from lasy.profiles.gaussian_profile import GaussianProfile
 from lasy.optical_elements import ParabolicMirror
+from lasy.profiles.gaussian_profile import GaussianProfile
 
 wavelength = 0.8e-6
 w0 = 5.0e-3  # m, initialized in near field

tests/test_speckles.py

@@ -1,11 +1,11 @@
 import numpy as np
+import pytest
+from scipy.constants import c
 
 np.random.seed(0)  # Fix random seed for reproducibility
 
 from lasy.laser import Laser
 from lasy.profiles.speckle_profile import SpeckleProfile
-import pytest
-from scipy.constants import c
 
 
 @pytest.mark.parametrize(

tests/test_t2z2t.py

@@ -1,12 +1,12 @@
 # -*- coding: utf-8 -*-
 
+import numpy as np
 import pytest
+from scipy.constants import c
 
-import numpy as np
 from lasy.laser import Laser
 from lasy.profiles.gaussian_profile import GaussianProfile
-from lasy.utils.laser_utils import import_from_z, export_to_z
-from scipy.constants import c
+from lasy.utils.laser_utils import export_to_z, import_from_z
 
 
 @pytest.fixture(scope="function")