Use isort with black to restructure imports

structuretoolkit/__init__.py

@@ -1,70 +1,76 @@
 # Analyse
 from structuretoolkit.analyse import (
-    get_distances_array,
     find_mic,
-    get_neighbors,
-    get_neighborhood,
-    get_equivalent_atoms,
-    get_steinhardt_parameters,
-    get_centro_symmetry_descriptors,
-    get_diamond_structure_descriptors,
-    get_adaptive_cna_descriptors,
-    get_voronoi_volumes,
     find_solids,
-    get_mean_positions,
+    get_adaptive_cna_descriptors,
     get_average_of_unique_labels,
+    get_centro_symmetry_descriptors,
+    get_cluster_positions,
+    get_delaunay_neighbors,
+    get_diamond_structure_descriptors,
+    get_distances_array,
+    get_equivalent_atoms,
     get_interstitials,
     get_layers,
-    get_voronoi_vertices,
-    get_voronoi_neighbors,
-    get_delaunay_neighbors,
-    get_cluster_positions,
+    get_mean_positions,
+    get_neighborhood,
+    get_neighbors,
+    get_steinhardt_parameters,
     get_strain,
     get_symmetry,
-    # for backwards compatibility
-    get_cluster_positions as cluster_positions,
-    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
-    get_steinhardt_parameters as get_steinhardt_parameter_structure,
-    get_centro_symmetry_descriptors as analyse_centro_symmetry,
-    get_diamond_structure_descriptors as analyse_diamond_structure,
-    get_adaptive_cna_descriptors as analyse_cna_adaptive,
-    get_voronoi_volumes as analyse_voronoi_volume,
-    find_solids as analyse_find_solids,
+    get_voronoi_neighbors,
+    get_voronoi_vertices,
+    get_voronoi_volumes,
 )
 
 # Build
 from structuretoolkit.build import (
-    grainboundary,
-    get_grainboundary_info,
     B2,
     C14,
     C15,
     C36,
     D03,
-    sqs_structures,
-    high_index_surface,
+    get_grainboundary_info,
     get_high_index_surface_info,
-    # for backwards compatibility
-    grainboundary as grainboundary_build,
-    get_grainboundary_info as grainboundary_info,
-    sqs_structures as get_sqs_structures,
-    get_high_index_surface_info as high_index_surface_info,
+    grainboundary,
+    high_index_surface,
+    sqs_structures,
 )
 
-# Visualize
-from structuretoolkit.visualize import plot3d
-
 # Common
 from structuretoolkit.common import (
+    SymmetryError,
+    apply_strain,
     ase_to_pymatgen,
-    pymatgen_to_ase,
     ase_to_pyscal,
+    center_coordinates_in_unit_cell,
     get_atomic_numbers,
     get_extended_positions,
     get_vertical_length,
     get_wrapped_coordinates,
+    pymatgen_to_ase,
     select_index,
-    center_coordinates_in_unit_cell,
-    apply_strain,
-    SymmetryError,
+)
+
+# Visualize
+from structuretoolkit.visualize import plot3d
+
+# Analyse - for backwards compatibility
+from structuretoolkit.analyse import (
+    find_solids as analyse_find_solids,
+    get_adaptive_cna_descriptors as analyse_cna_adaptive,
+    get_centro_symmetry_descriptors as analyse_centro_symmetry,
+    get_cluster_positions as cluster_positions,
+    get_diamond_structure_descriptors as analyse_diamond_structure,
+    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
+    get_steinhardt_parameters as get_steinhardt_parameter_structure,
+    get_voronoi_volumes as analyse_voronoi_volume,
+)
+
+# Build - for backwards compatibility
+from structuretoolkit.build import (
+    get_grainboundary_info as grainboundary_info,
+    get_high_index_surface_info as high_index_surface_info,
+    grainboundary as grainboundary_build,
+    sqs_structures as get_sqs_structures,
 )

structuretoolkit/analyse/__init__.py

@@ -1,24 +1,23 @@
-from structuretoolkit.analyse.distance import get_distances_array, find_mic
-from structuretoolkit.analyse.neighbors import get_neighbors, get_neighborhood
+from structuretoolkit.analyse.distance import find_mic, get_distances_array
+from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
 from structuretoolkit.analyse.phonopy import get_equivalent_atoms
 from structuretoolkit.analyse.pyscal import (
-    get_steinhardt_parameters,
+    find_solids,
+    get_adaptive_cna_descriptors,
     get_centro_symmetry_descriptors,
     get_diamond_structure_descriptors,
-    get_adaptive_cna_descriptors,
+    get_steinhardt_parameters,
     get_voronoi_volumes,
-    find_solids,
-    ase_to_pyscal,
 )
 from structuretoolkit.analyse.spatial import (
-    get_mean_positions,
     get_average_of_unique_labels,
+    get_cluster_positions,
+    get_delaunay_neighbors,
     get_interstitials,
     get_layers,
-    get_voronoi_vertices,
+    get_mean_positions,
     get_voronoi_neighbors,
-    get_delaunay_neighbors,
-    get_cluster_positions,
+    get_voronoi_vertices,
 )
 from structuretoolkit.analyse.strain import get_strain
 

structuretoolkit/analyse/neighbors.py

@@ -2,17 +2,18 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
+import itertools
+import warnings
+
 import numpy as np
 from scipy.sparse import coo_matrix
-from scipy.special import gamma
-from scipy.spatial.transform import Rotation
-from scipy.special import sph_harm
 from scipy.spatial import cKDTree
-import warnings
-import itertools
+from scipy.spatial.transform import Rotation
+from scipy.special import gamma, sph_harm
+
 from structuretoolkit.common.helper import (
-    get_extended_positions,
     get_average_of_unique_labels,
+    get_extended_positions,
 )
 
 __author__ = "Joerg Neugebauer, Sam Waseda"

structuretoolkit/analyse/pyscal.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 from ase.atoms import Atoms
+
 from structuretoolkit.common.pyscal import ase_to_pyscal
 
 __author__ = "Sarath Menon, Jan Janssen"

structuretoolkit/analyse/spatial.py

@@ -4,16 +4,15 @@
 
 import numpy as np
 from scipy.sparse import coo_matrix
-from scipy.spatial import Voronoi, Delaunay
-from scipy.spatial import ConvexHull
+from scipy.spatial import ConvexHull, Delaunay, Voronoi
+
+from structuretoolkit.analyse.neighbors import get_neighborhood
 from structuretoolkit.common.helper import (
+    get_average_of_unique_labels,
     get_extended_positions,
-    get_wrapped_coordinates,
     get_vertical_length,
-    get_average_of_unique_labels,
+    get_wrapped_coordinates,
 )
-from structuretoolkit.analyse.neighbors import get_neighborhood
-
 
 __author__ = "Joerg Neugebauer, Sam Waseda"
 __copyright__ = (

structuretoolkit/analyse/strain.py

@@ -1,5 +1,6 @@
 import numpy as np
 from scipy.spatial.transform import Rotation
+
 from structuretoolkit.analyse.neighbors import get_neighbors
 from structuretoolkit.analyse.pyscal import get_adaptive_cna_descriptors
 

structuretoolkit/analyse/symmetry.py

@@ -2,10 +2,11 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
+import ast
+
 import numpy as np
-from scipy.spatial import cKDTree
 import spglib
-import ast
+from scipy.spatial import cKDTree
 
 import structuretoolkit.common.helper
 from structuretoolkit.common.error import SymmetryError

structuretoolkit/common/__init__.py

@@ -1,12 +1,12 @@
-from structuretoolkit.common.pymatgen import ase_to_pymatgen, pymatgen_to_ase
-from structuretoolkit.common.pyscal import ase_to_pyscal
+from structuretoolkit.common.error import SymmetryError
 from structuretoolkit.common.helper import (
+    apply_strain,
+    center_coordinates_in_unit_cell,
     get_atomic_numbers,
     get_extended_positions,
     get_vertical_length,
     get_wrapped_coordinates,
     select_index,
-    center_coordinates_in_unit_cell,
-    apply_strain,
 )
-from structuretoolkit.common.error import SymmetryError
+from structuretoolkit.common.pymatgen import ase_to_pymatgen, pymatgen_to_ase
+from structuretoolkit.common.pyscal import ase_to_pyscal

structuretoolkit/common/helper.py

@@ -1,6 +1,6 @@
 import numpy as np
-from scipy.sparse import coo_matrix
 from ase.data import atomic_numbers
+from scipy.sparse import coo_matrix
 
 
 def get_atomic_numbers(structure):

structuretoolkit/visualize.py

@@ -2,9 +2,11 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
-import numpy as np
 import warnings
+
+import numpy as np
 from scipy.interpolate import interp1d
+
 from structuretoolkit.common.helper import get_atomic_numbers
 
 __author__ = "Joerg Neugebauer, Sudarsan Surendralal"