Linting fixes.

materialsproject · Jun 26, 2024 · bdbeadf · bdbeadf
1 parent 9b997fa
commit bdbeadf
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Showing 195 changed files with 121 additions and 316 deletions.
diff --git a/dev_scripts/chemenv/explicit_permutations.py b/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,

diff --git a/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py b/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,

diff --git a/dev_scripts/chemenv/get_plane_permutations_optimized.py b/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,

diff --git a/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py b/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,

diff --git a/dev_scripts/chemenv/test_algos.py b/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,

diff --git a/dev_scripts/chemenv/view_environment.py b/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,

diff --git a/dev_scripts/potcar_scrambler.py b/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

diff --git a/dev_scripts/update_pt_data.py b/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

diff --git a/tasks.py b/tasks.py
@@ -19,7 +19,6 @@
 import requests
 from invoke import task
 from monty.os import cd
-
 from pymatgen.core import __version__
 
 if TYPE_CHECKING:

diff --git a/tests/alchemy/test_filters.py b/tests/alchemy/test_filters.py
@@ -4,7 +4,6 @@
 from unittest import TestCase
 
 from monty.json import MontyDecoder
-
 from pymatgen.alchemy.filters import (
     ContainsSpecieFilter,
     RemoveDuplicatesFilter,

diff --git a/tests/alchemy/test_materials.py b/tests/alchemy/test_materials.py
@@ -4,7 +4,6 @@
 from copy import deepcopy
 
 import pytest
-
 from pymatgen.alchemy.filters import ContainsSpecieFilter
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.core import SETTINGS

diff --git a/tests/analysis/chemenv/connectivity/test_connected_components.py b/tests/analysis/chemenv/connectivity/test_connected_components.py
@@ -7,7 +7,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent
 from pymatgen.analysis.chemenv.connectivity.connectivity_finder import ConnectivityFinder
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode

diff --git a/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py b/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py
@@ -1,8 +1,6 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AdditionalConditionInt,
     AngleCutoffFloat,
@@ -11,6 +9,7 @@
     SimplestChemenvStrategy,
 )
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py b/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py
@@ -3,15 +3,14 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     AllCoordinationGeometries,
     CoordinationGeometry,
     ExplicitPermutationsAlgorithm,
     SeparationPlane,
 )
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py b/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py
@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,
@@ -13,6 +11,7 @@
 )
 from pymatgen.core.structure import Lattice, Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/coordination_environments/test_read_write.py b/tests/analysis/chemenv/coordination_environments/test_read_write.py
@@ -3,8 +3,6 @@
 import json
 
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,
@@ -23,6 +21,7 @@
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/coordination_environments/test_structure_environments.py b/tests/analysis/chemenv/coordination_environments/test_structure_environments.py
@@ -5,8 +5,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     MultiWeightsChemenvStrategy,
     SimplestChemenvStrategy,
@@ -18,6 +16,7 @@
 )
 from pymatgen.core import Species, Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/coordination_environments/test_voronoi.py b/tests/analysis/chemenv/coordination_environments/test_voronoi.py
@@ -3,7 +3,6 @@
 import random
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure

diff --git a/tests/analysis/chemenv/coordination_environments/test_weights.py b/tests/analysis/chemenv/coordination_environments/test_weights.py
@@ -3,8 +3,6 @@
 import json
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,
@@ -17,6 +15,7 @@
 )
 from pymatgen.analysis.chemenv.coordination_environments.structure_environments import StructureEnvironments
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py b/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py
@@ -5,10 +5,9 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "David Waroquiers"
 

diff --git a/tests/analysis/chemenv/utils/test_func_utils.py b/tests/analysis/chemenv/utils/test_func_utils.py
@@ -2,13 +2,12 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.chemenv.utils.func_utils import (
     CSMFiniteRatioFunction,
     CSMInfiniteRatioFunction,
     DeltaCSMRatioFunction,
 )
+from pytest import approx
 
 __author__ = "waroquiers"
 

diff --git a/tests/analysis/chemenv/utils/test_graph_utils.py b/tests/analysis/chemenv/utils/test_graph_utils.py
@@ -2,7 +2,6 @@
 
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
 from pymatgen.analysis.chemenv.utils.graph_utils import MultiGraphCycle, SimpleGraphCycle, get_delta
 from pymatgen.util.testing import PymatgenTest

diff --git a/tests/analysis/chemenv/utils/test_math_utils.py b/tests/analysis/chemenv/utils/test_math_utils.py
@@ -2,7 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.chemenv.utils.math_utils import (
     _cartesian_product,
     cosinus_step,

diff --git a/tests/analysis/diffraction/test_neutron.py b/tests/analysis/diffraction/test_neutron.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.diffraction.neutron import NDCalculator
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 """
 These calculated values were verified with VESTA and FullProf.

diff --git a/tests/analysis/diffraction/test_tem.py b/tests/analysis/diffraction/test_tem.py
@@ -6,12 +6,11 @@
 import pandas as pd
 import plotly.graph_objects as go
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.diffraction.tem import TEMCalculator
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "Frank Wan, Jason Liang"
 __copyright__ = "Copyright 2019, The Materials Project"

diff --git a/tests/analysis/diffraction/test_xrd.py b/tests/analysis/diffraction/test_xrd.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.diffraction.xrd import XRDCalculator
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 """
 TODO: Modify unittest doc.

diff --git a/tests/analysis/elasticity/test_elastic.py b/tests/analysis/elasticity/test_elastic.py
@@ -8,9 +8,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-from scipy.misc import central_diff_weights
-
 from pymatgen.analysis.elasticity.elastic import (
     ComplianceTensor,
     ElasticTensor,
@@ -29,6 +26,8 @@
 from pymatgen.core.tensors import Tensor
 from pymatgen.core.units import FloatWithUnit
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
+from scipy.misc import central_diff_weights
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/elasticity"
 

diff --git a/tests/analysis/elasticity/test_strain.py b/tests/analysis/elasticity/test_strain.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.elasticity.strain import Deformation, DeformedStructureSet, Strain, convert_strain_to_deformation
 from pymatgen.core.structure import Structure
 from pymatgen.core.tensors import Tensor

diff --git a/tests/analysis/elasticity/test_stress.py b/tests/analysis/elasticity/test_stress.py
@@ -3,11 +3,10 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.elasticity.strain import Deformation
 from pymatgen.analysis.elasticity.stress import Stress
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestStress(PymatgenTest):

diff --git a/tests/analysis/ferroelectricity/test_polarization.py b/tests/analysis/ferroelectricity/test_polarization.py
@@ -2,8 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.ferroelectricity.polarization import (
     EnergyTrend,
     Polarization,
@@ -14,6 +12,7 @@
 from pymatgen.io.vasp.inputs import Potcar
 from pymatgen.io.vasp.outputs import Outcar
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/vasp/fixtures/BTO_221_99_polarization"
 bto_folders = ["nonpolar_polarization"]

diff --git a/tests/analysis/interfaces/test_coherent_interface.py b/tests/analysis/interfaces/test_coherent_interface.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.interfaces.coherent_interfaces import (
     CoherentInterfaceBuilder,
     from_2d_to_3d,

diff --git a/tests/analysis/interfaces/test_substrate_analyzer.py b/tests/analysis/interfaces/test_substrate_analyzer.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.elasticity.elastic import ElasticTensor
 from pymatgen.analysis.interfaces.substrate_analyzer import SubstrateAnalyzer
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

diff --git a/tests/analysis/interfaces/test_zsl.py b/tests/analysis/interfaces/test_zsl.py
@@ -2,8 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_array_equal
-from pytest import approx
-
 from pymatgen.analysis.interfaces.zsl import (
     ZSLGenerator,
     fast_norm,
@@ -14,6 +12,7 @@
 )
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "Shyam Dwaraknath"
 __copyright__ = "Copyright 2016, The Materials Project"