pre-commit auto-fixes

dev_scripts/chemenv/explicit_permutations.py

@@ -10,7 +10,6 @@
 import os
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     AllCoordinationGeometries,
     ExplicitPermutationsAlgorithm,

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -9,7 +9,6 @@
 import json
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -15,7 +15,6 @@
 
 import numpy as np
 import tabulate
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -8,7 +8,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,

dev_scripts/chemenv/test_algos.py

@@ -8,7 +8,6 @@
 from random import shuffle
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/view_environment.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     SEPARATION_PLANE,
     AllCoordinationGeometries,

dev_scripts/potcar_scrambler.py

@@ -9,7 +9,6 @@
 import numpy as np
 from monty.os.path import zpath
 from monty.serialization import zopen
-
 from pymatgen.core import SETTINGS
 from pymatgen.io.vasp import Potcar, PotcarSingle
 from pymatgen.io.vasp.sets import _load_yaml_config

dev_scripts/update_pt_data.py

@@ -11,9 +11,8 @@
 import requests
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
-from ruamel import yaml
-
 from pymatgen.core import Element, get_el_sp
+from ruamel import yaml
 
 try:
     from bs4 import BeautifulSoup

src/pymatgen/alchemy/filters.py

@@ -7,15 +7,13 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core import get_el_sp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 
 class AbstractStructureFilter(MSONable, abc.ABC):

src/pymatgen/alchemy/materials.py

@@ -12,7 +12,6 @@
 from warnings import warn
 
 from monty.json import MSONable, jsanitize
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.cif import CifParser
 from pymatgen.io.vasp.inputs import Poscar
@@ -24,9 +23,8 @@
     from collections.abc import Sequence
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.alchemy.filters import AbstractStructureFilter
+    from typing_extensions import Self
 
 
 class TransformedStructure(MSONable):

src/pymatgen/alchemy/transmuters.py

@@ -21,9 +21,8 @@
     from collections.abc import Sequence
     from typing import Callable
 
-    from typing_extensions import Self
-
     from pymatgen.alchemy.filters import AbstractStructureFilter
+    from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, Will Richards"
 __copyright__ = "Copyright 2012, The Materials Project"

src/pymatgen/analysis/adsorption.py

@@ -12,8 +12,6 @@
 from matplotlib import patches
 from matplotlib.path import Path
 from monty.serialization import loadfn
-from scipy.spatial import Delaunay
-
 from pymatgen import vis
 from pymatgen.analysis.local_env import VoronoiNN
 from pymatgen.analysis.structure_matcher import StructureMatcher
@@ -22,13 +20,13 @@
 from pymatgen.core.surface import generate_all_slabs
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.coord import in_coord_list_pbc
+from scipy.spatial import Delaunay
 
 if TYPE_CHECKING:
     import matplotlib.pyplot as plt
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.surface import Slab
+    from typing_extensions import Self
 
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2016, The Materials Project"

src/pymatgen/analysis/bond_dissociation.py

@@ -8,7 +8,6 @@
 
 import networkx as nx
 from monty.json import MSONable
-
 from pymatgen.analysis.fragmenter import open_ring
 from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
 from pymatgen.analysis.local_env import OpenBabelNN

src/pymatgen/analysis/bond_valence.py

@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.serialization import loadfn
-
 from pymatgen.core import Element, Species, get_el_sp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 

src/pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -13,7 +13,6 @@
 from monty.json import MSONable, jsanitize
 from networkx.algorithms.components import is_connected
 from networkx.algorithms.traversal import bfs_tree
-
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
 from pymatgen.analysis.chemenv.utils.chemenv_errors import ChemenvError
 from pymatgen.analysis.chemenv.utils.graph_utils import get_delta

src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py

@@ -5,7 +5,6 @@
 import logging
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity
 
 __author__ = "David Waroquiers"

src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py

@@ -9,7 +9,6 @@
 import networkx as nx
 import numpy as np
 from monty.json import MSONable, jsanitize
-
 from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import get_environment_node
 from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments

src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -13,8 +13,6 @@
 
 import numpy as np
 from monty.json import MSONable
-from scipy.stats import gmean
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.analysis.chemenv.utils.chemenv_errors import EquivalentSiteSearchError
@@ -29,6 +27,7 @@
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.sites import PeriodicSite
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from scipy.stats import gmean
 
 if TYPE_CHECKING:
     from typing import ClassVar

src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -23,7 +23,6 @@
 
 import numpy as np
 from numpy.linalg import norm, svd
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import MultiWeightsChemenvStrategy
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (

src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -17,7 +17,6 @@
 from matplotlib.gridspec import GridSpec
 from matplotlib.patches import Polygon
 from monty.json import MontyDecoder, MSONable, jsanitize
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.analysis.chemenv.utils.chemenv_errors import ChemenvError

src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py

@@ -9,8 +9,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from monty.json import MSONable
-from scipy.spatial import Voronoi
-
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import (
     get_lower_and_upper_f,
     rectangle_surface_intersection,
@@ -20,6 +18,7 @@
 from pymatgen.analysis.chemenv.utils.math_utils import normal_cdf_step
 from pymatgen.core.sites import PeriodicSite
 from pymatgen.core.structure import Structure
+from scipy.spatial import Voronoi
 
 if TYPE_CHECKING:
     from typing_extensions import Self

src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -7,12 +7,11 @@
 
 import numpy as np
 from numpy.linalg import norm
+from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError
 from scipy.integrate import quad
 from scipy.interpolate import UnivariateSpline
 from scipy.spatial import ConvexHull
 
-from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError
-
 if TYPE_CHECKING:
     from typing import Callable
 

src/pymatgen/analysis/chemenv/utils/func_utils.py

@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.utils.math_utils import (
     power2_decreasing_exp,
     power2_inverse_decreasing,

src/pymatgen/analysis/chemenv/utils/scripts_utils.py

@@ -6,7 +6,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     SimpleAbundanceChemenvStrategy,
     SimplestChemenvStrategy,

src/pymatgen/analysis/chempot_diagram.py

@@ -33,13 +33,12 @@
 import plotly.express as px
 from monty.json import MSONable
 from plotly.graph_objects import Figure, Mesh3d, Scatter, Scatter3d
-from scipy.spatial import ConvexHull, HalfspaceIntersection
-
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.core.composition import Composition, Element
 from pymatgen.util.coord import Simplex
 from pymatgen.util.due import Doi, due
 from pymatgen.util.string import htmlify
+from scipy.spatial import ConvexHull, HalfspaceIntersection
 
 if TYPE_CHECKING:
     from pymatgen.entries.computed_entries import ComputedEntry

src/pymatgen/analysis/cost.py

@@ -17,7 +17,6 @@
 
 import scipy.constants as const
 from monty.design_patterns import singleton
-
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.core import Composition, Element
 from pymatgen.util.provenance import is_valid_bibtex

src/pymatgen/analysis/diffraction/core.py

@@ -8,7 +8,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.util.plotting import add_fig_kwargs, pretty_plot
 

src/pymatgen/analysis/diffraction/neutron.py

@@ -8,7 +8,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.diffraction.core import (
     AbstractDiffractionPatternCalculator,
     DiffractionPattern,

src/pymatgen/analysis/diffraction/tem.py

@@ -11,15 +11,13 @@
 import pandas as pd
 import plotly.graph_objects as go
 import scipy.constants as sc
-
 from pymatgen.analysis.diffraction.core import AbstractDiffractionPatternCalculator
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.string import latexify_spacegroup, unicodeify_spacegroup
 from pymatgen.util.typing import Tuple3Ints
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
-
     from pymatgen.core import Structure
 
 __author__ = "Frank Wan, Jason Liang"

src/pymatgen/analysis/diffraction/xrd.py

@@ -8,7 +8,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.diffraction.core import (
     AbstractDiffractionPatternCalculator,
     DiffractionPattern,

src/pymatgen/analysis/dimensionality.py

@@ -29,7 +29,6 @@
 import networkx as nx
 import numpy as np
 from networkx.readwrite import json_graph
-
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from pymatgen.analysis.local_env import JmolNN
 from pymatgen.analysis.structure_analyzer import get_max_bond_lengths

src/pymatgen/analysis/elasticity/elastic.py

@@ -13,24 +13,22 @@
 
 import numpy as np
 import sympy as sp
-from scipy.integrate import quad
-from scipy.optimize import root
-from scipy.special import factorial
-
 from pymatgen.analysis.elasticity.strain import Strain
 from pymatgen.analysis.elasticity.stress import Stress
 from pymatgen.core.tensors import DEFAULT_QUAD, SquareTensor, Tensor, TensorCollection, get_uvec
 from pymatgen.core.units import Unit
 from pymatgen.util.due import Doi, due
+from scipy.integrate import quad
+from scipy.optimize import root
+from scipy.special import factorial
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 
 __author__ = "Joseph Montoya"

src/pymatgen/analysis/elasticity/strain.py

@@ -12,7 +12,6 @@
 
 import numpy as np
 import scipy
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.tensors import SquareTensor, symmetry_reduce
 
@@ -21,9 +20,8 @@
     from typing import Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.structure import Structure
+    from typing_extensions import Self
 
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"

src/pymatgen/analysis/elasticity/stress.py

@@ -9,7 +9,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.core.tensors import SquareTensor
 
 if TYPE_CHECKING: