Merge pull request #2415 from janosh/isort

isort

.pre-commit-config.yaml

@@ -13,10 +13,16 @@ repos:
     hooks:
       - id: black
 
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.1.0
     hooks:
       - id: check-yaml
+        exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 

dev_scripts/chemenv/check_new_coordination_geometry.py

@@ -1,7 +1,12 @@
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
 import logging
 
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+)
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
+    LocalGeometryFinder,
+)
+
 allcg = AllCoordinationGeometries()
 
 lgf = LocalGeometryFinder()

dev_scripts/chemenv/explicit_permutations.py

@@ -13,16 +13,21 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import ExplicitPermutationsAlgorithm
-
-import numpy as np
 import itertools
 import json
 import os
 
+import numpy as np
+
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+    ExplicitPermutationsAlgorithm,
+)
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
+    AbstractGeometry,
+    LocalGeometryFinder,
+)
+
 
 class Algo:
     pass

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -6,15 +6,20 @@
 with the separation plane algorithms (typically with coordination numbers >= 6)
 """
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane, collinear
-
-import numpy as np
 import itertools
 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,
+    LocalGeometryFinder,
+)
+from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane, collinear
+
 if __name__ == "__main__":
 
     # Choose the geometry

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -13,21 +13,25 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
-from math import factorial
-
-import numpy as np
 import itertools
-from random import shuffle
 import json
 import os
-import tabulate
 import time
-
+from math import factorial
 from optparse import OptionParser
+from random import shuffle
+
+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,
+    LocalGeometryFinder,
+)
+from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
 
 
 # Printing functions depending on the printing volume option

dev_scripts/chemenv/plane_multiplicity.py

@@ -12,7 +12,9 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+)
 
 if __name__ == "__main__":
 

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -12,26 +12,31 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.core.lattice import Lattice
-from pymatgen.core.structure import Structure
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
-
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import NormalizedAngleDistanceNbSetWeight
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SelfCSMNbSetWeight
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import DeltaCSMNbSetWeight
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import CNBiasNbSetWeight
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import DistanceAngleAreaNbSetWeight
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import AngleNbSetWeight
-
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import MultiWeightsChemenvStrategy
-
-import numpy as np
-import matplotlib.pyplot as plt
 import copy
 import json
 
+import matplotlib.pyplot as plt
+import numpy as np
+
+from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
+    AngleNbSetWeight,
+    CNBiasNbSetWeight,
+    DeltaCSMNbSetWeight,
+    DistanceAngleAreaNbSetWeight,
+    MultiWeightsChemenvStrategy,
+    NormalizedAngleDistanceNbSetWeight,
+    SelfCSMNbSetWeight,
+)
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+)
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
+    AbstractGeometry,
+    LocalGeometryFinder,
+)
+from pymatgen.core.lattice import Lattice
+from pymatgen.core.structure import Structure
+
 allcg = AllCoordinationGeometries()
 
 

dev_scripts/chemenv/test_algos.py

@@ -13,16 +13,20 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
+import itertools
+import time
 from math import factorial
+from random import shuffle
 
 import numpy as np
-import itertools
-from random import shuffle
-import time
 
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+)
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
+    AbstractGeometry,
+    LocalGeometryFinder,
+)
 
 if __name__ == "__main__":
 

dev_scripts/chemenv/test_algos_all_geoms.py

@@ -13,14 +13,17 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import AbstractGeometry
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from math import factorial
-
 import itertools
+from math import factorial
 from random import shuffle
 
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    AllCoordinationGeometries,
+)
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
+    AbstractGeometry,
+    LocalGeometryFinder,
+)
 
 if __name__ == "__main__":
 

dev_scripts/chemenv/view_environment.py

@@ -12,13 +12,15 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
-from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import SEPARATION_PLANE
-from pymatgen.analysis.chemenv.utils.scripts_utils import visualize
-from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
-
 import numpy as np
 
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
+    SEPARATION_PLANE,
+    AllCoordinationGeometries,
+)
+from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
+from pymatgen.analysis.chemenv.utils.scripts_utils import visualize
+
 if __name__ == "__main__":
     print(
         "+-------------------------------------------------------+\n"

docs_rst/conf.py

@@ -10,8 +10,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -21,7 +21,7 @@
 sys.path.insert(0, os.path.dirname("../pymatgen"))
 sys.path.insert(0, os.path.dirname("../.."))
 
-from pymatgen.core import __version__, __author__, __file__
+from pymatgen.core import __author__, __file__, __version__
 
 # -- General configuration -----------------------------------------------------
 

pymatgen/alchemy/materials.py

@@ -151,9 +151,8 @@ def append_filter(self, structure_filter):
         Adds a filter.
 
         Args:
-            structure_filter (StructureFilter): A filter implementating the
-                AbstractStructureFilter API. Tells transmuter waht structures
-                to retain.
+            structure_filter (StructureFilter): A filter implementing the
+                AbstractStructureFilter API. Tells transmuter what structures to retain.
         """
         hdict = structure_filter.as_dict()
         hdict["input_structure"] = self.final_structure.as_dict()

pymatgen/alchemy/tests/test_materials.py

@@ -6,9 +6,9 @@
 import unittest
 import warnings
 
-from pymatgen.core import SETTINGS
 from pymatgen.alchemy.filters import ContainsSpecieFilter
 from pymatgen.alchemy.materials import TransformedStructure
+from pymatgen.core import SETTINGS
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.sets import MPRelaxSet
 from pymatgen.transformations.standard_transformations import (

pymatgen/alchemy/tests/test_transmuters.py

@@ -5,7 +5,6 @@
 import os
 import warnings
 
-from pymatgen.util.testing import PymatgenTest
 from pymatgen.alchemy.filters import ContainsSpecieFilter
 from pymatgen.alchemy.transmuters import CifTransmuter, PoscarTransmuter
 from pymatgen.transformations.advanced_transformations import SuperTransformation
@@ -14,6 +13,7 @@
     RemoveSpeciesTransformation,
     SubstitutionTransformation,
 )
+from pymatgen.util.testing import PymatgenTest
 
 
 class CifTransmuterTest(PymatgenTest):

pymatgen/analysis/adsorption.py

@@ -17,10 +17,10 @@
 from scipy.spatial import Delaunay
 
 from pymatgen import vis
-from pymatgen.core.structure import Structure
 from pymatgen.analysis.local_env import VoronoiNN
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core.operations import SymmOp
+from pymatgen.core.structure import Structure
 from pymatgen.core.surface import generate_all_slabs
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.coord import in_coord_list_pbc
@@ -572,7 +572,7 @@ def generate_substitution_structures(
 
         target_species = target_species or []
 
-        # Get symmetrized structure in case we want to substitue both sides
+        # Get symmetrized structure in case we want to substitute both sides
         sym_slab = SpacegroupAnalyzer(self.slab).get_symmetrized_structure()
 
         # Define a function for substituting a site

pymatgen/analysis/bond_dissociation.py

@@ -275,7 +275,7 @@ def search_fragment_entries(self, frag):
         """
         Search all fragment entries for those isomorphic to the given fragment.
         We distinguish between entries where both initial and final molgraphs are isomorphic to the
-        given fragment (entries) vs those where only the intial molgraph is isomorphic to the given
+        given fragment (entries) vs those where only the initial molgraph is isomorphic to the given
         fragment (initial_entries) vs those where only the final molgraph is isomorphic (final_entries)
 
         Args:

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -871,7 +871,7 @@ def _retuplify_edgedata(edata):
             edata (dict): Edge data dictionary with possibly the above tuples as lists.
 
         Returns:
-            dict: Edge data dictionary with the lists tranformed back into tuples when applicable.
+            dict: Edge data dictionary with the lists transformed back into tuples when applicable.
         """
         edata["delta"] = tuple(edata["delta"])
         edata["ligands"] = [tuple([lig[0], tuple(lig[1]), tuple(lig[2])]) for lig in edata["ligands"]]

pymatgen/analysis/chemenv/connectivity/environment_nodes.py

@@ -55,7 +55,7 @@ def __eq__(self, other):
 
     def __lt__(self, other):
         # This simple "Less Than" operator allows to strictly sort environment nodes in a graph.
-        # This is useful (and actually neeeded) in the definition of the cycles but does not have
+        # This is useful (and actually needed) in the definition of the cycles but does not have
         # any real meaning of a "lower value" environment node.
         return self.isite < other.isite
 

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -590,7 +590,7 @@ def __init__(
             algorithms: Algorithms used to identify this coordination geometry.
             equivalent_indices: The equivalent sets of indices in this coordination geometry (can be used to skip
                 equivalent permutations that have already been performed).
-            neighbors_sets_hints: Neighors sets hints for this coordination geometry.
+            neighbors_sets_hints: Neighbors sets hints for this coordination geometry.
         """
         self._mp_symbol = mp_symbol
         self.name = name