pre-commit auto-fixes

dev_scripts/chemenv/explicit_permutations.py

@@ -10,6 +10,7 @@
 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

@@ -9,6 +9,7 @@
 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

@@ -15,6 +15,7 @@
 
 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

@@ -8,6 +8,7 @@
 
 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

@@ -8,6 +8,7 @@
 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

@@ -3,6 +3,7 @@
 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

@@ -9,6 +9,7 @@
 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 +11,10 @@
 import requests
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
-from pymatgen.core import Element, get_el_sp
 from ruamel import yaml
 
+from pymatgen.core import Element, get_el_sp
+
 try:
  from bs4 import BeautifulSoup
 except ImportError:

dev_scripts/update_spacegroup_data.py

@@ -12,6 +12,7 @@
 import sys
 
 from monty.serialization import dumpfn, loadfn
+
 from pymatgen.symmetry.groups import PointGroup
 
 __author__ = "Katharina Ueltzen @kaueltzen"

pymatgen/core/tests/test_structure.py

@@ -644,11 +644,11 @@ def test_get_all_neighbors_small_cutoff(self):
  )
  all_nn = s.get_all_neighbors(1e-5, True)
  assert len(all_nn) == len(s)
- assert [] == all_nn[0]
+ assert all_nn[0] == []
 
  all_nn = s.get_all_neighbors(0, True)
  assert len(all_nn) == len(s)
- assert [] == all_nn[0]
+ assert all_nn[0] == []
 
  def test_coincide_sites(self):
  s = Structure(

src/pymatgen/alchemy/filters.py

@@ -7,14 +7,16 @@
 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 pymatgen.core import Structure
  from typing_extensions import Self
 
+ from pymatgen.core import Structure
+
 
 class AbstractStructureFilter(MSONable, abc.ABC):
  """Structures that return True when passed to the test() method are retained during

src/pymatgen/alchemy/materials.py

@@ -12,6 +12,7 @@
 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
@@ -23,9 +24,10 @@
  from collections.abc import Sequence
  from typing import Any
 
- from pymatgen.alchemy.filters import AbstractStructureFilter
  from typing_extensions import Self
 
+ from pymatgen.alchemy.filters import AbstractStructureFilter
+
 
 class TransformedStructure(MSONable):
  """Container for new structures that include history of transformations.

src/pymatgen/alchemy/transmuters.py

@@ -21,9 +21,10 @@
  from collections.abc import Sequence
  from typing import Callable
 
- from pymatgen.alchemy.filters import AbstractStructureFilter
  from typing_extensions import Self
 
+ from pymatgen.alchemy.filters import AbstractStructureFilter
+
 __author__ = "Shyue Ping Ong, Will Richards"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "0.1"

src/pymatgen/analysis/adsorption.py

@@ -12,6 +12,8 @@
 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
@@ -20,14 +22,14 @@
 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 pymatgen.core.surface import Slab
  from typing_extensions import Self
 
+ from pymatgen.core.surface import Slab
+
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2016, The Materials Project"
 __version__ = "0.1"

src/pymatgen/analysis/bond_dissociation.py

@@ -8,6 +8,7 @@
 
 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

@@ -11,6 +11,7 @@
 
 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

@@ -13,6 +13,7 @@
 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

@@ -5,6 +5,7 @@
 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

@@ -9,6 +9,7 @@
 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

@@ -13,6 +13,8 @@
 
 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
@@ -27,7 +29,6 @@
 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

@@ -23,6 +23,7 @@
 
 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

@@ -17,6 +17,7 @@
 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

@@ -9,6 +9,8 @@
 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,
@@ -18,7 +20,6 @@
 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

@@ -7,11 +7,12 @@
 
 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

@@ -5,6 +5,7 @@
 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

@@ -6,6 +6,7 @@
 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

@@ -33,12 +33,13 @@
 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

@@ -17,6 +17,7 @@
 
 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

@@ -8,6 +8,7 @@
 
 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

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

src/pymatgen/analysis/diffraction/tem.py

@@ -11,13 +11,15 @@
 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

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

src/pymatgen/analysis/dimensionality.py

@@ -29,6 +29,7 @@
 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

@@ -13,23 +13,25 @@
 
 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 pymatgen.core import Structure
  from typing_extensions import Self
 
+ from pymatgen.core import Structure
+
 
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"