Breaking typo fix: Targe(tt->t)edPenaltiedAbundanceChemenvStrategy

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -606,10 +606,10 @@ def get_site_neighbors(self, site, isite=None, dequivsite=None, dthissite=None,
         )
 
         nb_set = self.structure_environments.neighbors_sets[isite][cn_map[0]][cn_map[1]]
-        eqsite_ps = nb_set.neighb_sites
+        eq_site_ps = nb_set.neighb_sites
 
         coordinated_neighbors = []
-        for ps in eqsite_ps:
+        for ps in eq_site_ps:
             coords = mysym.operate(ps.frac_coords + dequivsite) + dthissite
             ps_site = PeriodicSite(ps._species, coords, ps._lattice)
             coordinated_neighbors.append(ps_site)
@@ -1029,7 +1029,7 @@ def from_dict(cls, d):
         return cls(additional_condition=d["additional_condition"])
 
 
-class TargettedPenaltiedAbundanceChemenvStrategy(SimpleAbundanceChemenvStrategy):
+class TargetedPenaltiedAbundanceChemenvStrategy(SimpleAbundanceChemenvStrategy):
     """
     Simple ChemenvStrategy using the neighbors that are the most "abundant" in the grid of angle and distance
     parameters for the definition of neighbors in the Voronoi approach, with a bias for a given list of target
@@ -1050,7 +1050,7 @@ def __init__(
         max_csm=5.0,
         symmetry_measure_type=AbstractChemenvStrategy.DEFAULT_SYMMETRY_MEASURE_TYPE,
     ):
-        """Initializes strategy.
+        """Initialize strategy.
 
         Not yet implemented.
         :param structure_environments:
@@ -1072,7 +1072,7 @@ def __init__(
         self.target_environments = target_environments
         self.target_penalty_type = target_penalty_type
         self.max_csm = max_csm
-        raise NotImplementedError("TargettedPenaltiedAbundanceChemenvStrategy not yet implemented")
+        raise NotImplementedError("TargetedPenaltiedAbundanceChemenvStrategy not yet implemented")
 
     def get_site_coordination_environment(
         self,
@@ -1157,10 +1157,10 @@ def uniquely_determines_coordination_environments(self):
 
     def as_dict(self):
         """
-        Bson-serializable dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object.
+        Bson-serializable dict representation of the TargetedPenaltiedAbundanceChemenvStrategy object.
 
         Returns:
-            Bson-serializable dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object.
+            Bson-serializable dict representation of the TargetedPenaltiedAbundanceChemenvStrategy object.
         """
         return {
             "@module": type(self).__module__,
@@ -1187,12 +1187,12 @@ def __eq__(self, other: object) -> bool:
     @classmethod
     def from_dict(cls, d):
         """
-        Reconstructs the TargettedPenaltiedAbundanceChemenvStrategy object from a dict representation of the
-        TargettedPenaltiedAbundanceChemenvStrategy object created using the as_dict method.
-        :param d: dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object
+        Reconstructs the TargetedPenaltiedAbundanceChemenvStrategy object from a dict representation of the
+        TargetedPenaltiedAbundanceChemenvStrategy object created using the as_dict method.
+        :param d: dict representation of the TargetedPenaltiedAbundanceChemenvStrategy object
 
         Returns:
-            TargettedPenaltiedAbundanceChemenvStrategy object.
+            TargetedPenaltiedAbundanceChemenvStrategy object.
         """
         return cls(
             additional_condition=d["additional_condition"],
@@ -1678,7 +1678,7 @@ def __init__(
         delta_cn_weight_estimators=None,
         symmetry_measure_type=DEFAULT_SYMMETRY_MEASURE_TYPE,
     ):
-        """Initialize SelfCSMNbSetWeight.
+        """Initialize DeltaCSMNbSetWeight.
 
         :param effective_csm_estimator: Ratio function used for the effective CSM (comparison between neighbors sets).
         :param weight_estimator: Weight estimator within a given neighbors set.
@@ -1815,7 +1815,7 @@ def delta_cn_specifics(
         symmetry_measure_type="csm_wcs_ctwcc",
         effective_csm_estimator=DEFAULT_EFFECTIVE_CSM_ESTIMATOR,
     ):
-        """Initializes DeltaCSMNbSetWeight from specific coordination number differences.
+        """Initialize DeltaCSMNbSetWeight from specific coordination number differences.
 
         :param delta_csm_mins: Minimums for each coordination number.
         :param delta_csm_maxs: Maximums for each coordination number.
@@ -1928,9 +1928,6 @@ def __eq__(self, other: object) -> bool:
 
         return self.cn_weights == other.cn_weights and self.initialization_options == other.initialization_options
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """MSONable dict."""
         return {
@@ -1956,7 +1953,7 @@ def from_dict(cls, dct):
 
     @classmethod
     def linearly_equidistant(cls, weight_cn1, weight_cn13):
-        """Initializes linearly equidistant weights for each coordination.
+        """Initialize linearly equidistant weights for each coordination.
 
         :param weight_cn1: Weight of coordination 1.
         :param weight_cn13: Weight of coordination 13.
@@ -1975,7 +1972,7 @@ def linearly_equidistant(cls, weight_cn1, weight_cn13):
 
     @classmethod
     def geometrically_equidistant(cls, weight_cn1, weight_cn13):
-        """Initializes geometrically equidistant weights for each coordination.
+        """Initialize geometrically equidistant weights for each coordination.
 
         :param weight_cn1: Weight of coordination 1.
         :param weight_cn13: Weight of coordination 13.
@@ -1994,7 +1991,7 @@ def geometrically_equidistant(cls, weight_cn1, weight_cn13):
 
     @classmethod
     def explicit(cls, cn_weights):
-        """Initializes weights explicitly for each coordination.
+        """Initialize weights explicitly for each coordination.
 
         :param cn_weights: Weights for each coordination.
 
@@ -2008,7 +2005,7 @@ def explicit(cls, cn_weights):
 
     @classmethod
     def from_description(cls, dct):
-        """Initializes weights from description.
+        """Initialize weights from description.
 
         :param dct: Dictionary description.
 
@@ -2225,9 +2222,6 @@ def __eq__(self, other: object) -> bool:
             and self.additional_condition == other.additional_condition
         )
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """MSONable dict."""
         return {
@@ -2298,9 +2292,6 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
     def __eq__(self, other: object) -> bool:
         return isinstance(other, type(self))
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """MSONable dict."""
         return {
@@ -2365,9 +2356,6 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
     def __eq__(self, other: object) -> bool:
         return isinstance(other, type(self))
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """MSONable dict."""
         return {
@@ -2446,9 +2434,6 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
     def __eq__(self, other: object) -> bool:
         return isinstance(other, type(self))
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """MSOnable dict."""
         return {
@@ -2530,9 +2515,6 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
     def __eq__(self, other: object) -> bool:
         return isinstance(other, type(self))
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """MSONable dict."""
         return {
@@ -2813,9 +2795,6 @@ def __eq__(self, other: object) -> bool:
             and self.ce_estimator == other.ce_estimator
         )
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """
         Bson-serializable dict representation of the WeightedNbSetChemenvStrategy object.
@@ -2982,9 +2961,6 @@ def __eq__(self, other: object) -> bool:
             and self.ce_estimator == other.ce_estimator
         )
 
-    def __ne__(self, other):
-        return not self == other
-
     def as_dict(self):
         """
         Returns:

pymatgen/analysis/chemenv/utils/scripts_utils.py

@@ -7,7 +7,12 @@
 
 import numpy as np
 
-from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
+from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
+    AbstractChemenvStrategy,
+    SimpleAbundanceChemenvStrategy,
+    SimplestChemenvStrategy,
+    TargetedPenaltiedAbundanceChemenvStrategy,
+)
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     UNCLEAR_ENVIRONMENT_SYMBOL,
     AllCoordinationGeometries,
@@ -38,12 +43,11 @@
 __email__ = "[email protected]"
 __date__ = "Feb 20, 2016"
 
-strategies_class_lookup = {}
-strategies_class_lookup["SimplestChemenvStrategy"] = SimplestChemenvStrategy
-
-
-# strategies_class_lookup['SimpleAbundanceChemenvStrategy'] = SimpleAbundanceChemenvStrategy
-# strategies_class_lookup['TargettedPenaltiedAbundanceChemenvStrategy'] = TargettedPenaltiedAbundanceChemenvStrategy
+strategies_class_lookup: dict[str, AbstractChemenvStrategy] = {
+    "SimplestChemenvStrategy": SimplestChemenvStrategy,  # type: ignore
+    "SimpleAbundanceChemenvStrategy": SimpleAbundanceChemenvStrategy,  # type: ignore
+    "TargetedPenaltiedAbundanceChemenvStrategy": TargetedPenaltiedAbundanceChemenvStrategy,  # type: ignore
+}
 
 
 def draw_cg(

tasks.py

@@ -9,12 +9,12 @@
 from __future__ import annotations
 
 import datetime
-import glob
 import json
 import os
 import re
 import subprocess
 import webbrowser
+from glob import glob
 
 import requests
 from invoke import task
@@ -41,7 +41,7 @@ def make_doc(ctx):
         ctx.run("rm *.rst", warn=True)
         ctx.run("cp markdown/pymatgen*.md .")
         ctx.run("rm pymatgen*tests*.md", warn=True)
-        for fn in glob.glob("pymatgen*.md"):
+        for fn in glob("pymatgen*.md"):
             with open(fn) as f:
                 lines = [line.rstrip() for line in f if "Submodules" not in line]
             if fn == "pymatgen.md":
@@ -319,7 +319,7 @@ def check_egg_sources_txt_for_completeness():
             raise ValueError(f"{src_file} does not exist!")
 
     for ext in ("py", "json", "json.gz", "yaml", "csv"):
-        for filepath in glob.glob(f"pymatgen/**/*.{ext}", recursive=True):
+        for filepath in glob(f"pymatgen/**/*.{ext}", recursive=True):
             if "/tests/" in filepath or "dao" in filepath:
                 continue
             if filepath not in sources:

tests/analysis/test_ewald.py

@@ -14,13 +14,13 @@
 class TestEwaldSummation(unittest.TestCase):
     def setUp(self):
         filepath = f"{TEST_FILES_DIR}/POSCAR"
-        p = Poscar.from_file(filepath, check_for_POTCAR=False)
-        self.original_s = p.structure
-        self.s = self.original_s.copy()
-        self.s.add_oxidation_state_by_element({"Li": 1, "Fe": 2, "P": 5, "O": -2})
+        poscar = Poscar.from_file(filepath, check_for_POTCAR=False)
+        self.original_struct = poscar.structure
+        self.struct = self.original_struct.copy()
+        self.struct.add_oxidation_state_by_element({"Li": 1, "Fe": 2, "P": 5, "O": -2})
 
     def test_init(self):
-        ham = EwaldSummation(self.s, compute_forces=True)
+        ham = EwaldSummation(self.struct, compute_forces=True)
         assert ham.real_space_energy == approx(-502.23549897772602, abs=1e-4)
         assert ham.reciprocal_space_energy == approx(6.1541071599534654, abs=1e-4)
         assert ham.point_energy == approx(-620.22598358035918, abs=1e-4)
@@ -36,10 +36,10 @@ def test_init(self):
             ValueError,
             match="Ewald summation can only be performed on structures that are either oxidation state decorated",
         ):
-            EwaldSummation(self.original_s)
+            EwaldSummation(self.original_struct)
         # try sites with charge.
         charges = []
-        for site in self.original_s:
+        for site in self.original_struct:
             if site.specie.symbol == "Li":
                 charges.append(1)
             elif site.specie.symbol == "Fe":
@@ -49,12 +49,12 @@ def test_init(self):
             else:
                 charges.append(-2)
 
-        self.original_s.add_site_property("charge", charges)
-        ham2 = EwaldSummation(self.original_s)
+        self.original_struct.add_site_property("charge", charges)
+        ham2 = EwaldSummation(self.original_struct)
         assert ham2.real_space_energy == approx(-502.23549897772602, abs=1e-4)
 
     def test_from_dict(self):
-        ham = EwaldSummation(self.s, compute_forces=True)
+        ham = EwaldSummation(self.struct, compute_forces=True)
         ham2 = EwaldSummation.from_dict(ham.as_dict())
         assert ham._real is None
         assert not ham._initialized
@@ -71,7 +71,7 @@ def test_from_dict(self):
         assert np.array_equal(ham.total_energy_matrix, ham2.total_energy_matrix)
 
     def test_as_dict(self):
-        ham = EwaldSummation(self.s, compute_forces=True)
+        ham = EwaldSummation(self.struct, compute_forces=True)
         d = ham.as_dict()
         assert d["compute_forces"]
         assert d["eta"] == ham._eta

tests/analysis/test_molecule_matcher.py

@@ -84,7 +84,7 @@ def generate_Si_cluster():
     mol = Molecule.from_sites(struct)
     XYZ(mol).write_file(f"{test_dir}/Si_cluster.xyz")
 
-    # Rorate the whole molecule
+    # Rotate the whole molecule
     mol_rotated = mol.copy()
     rotate(mol_rotated, seed=42)
     XYZ(mol_rotated).write_file(f"{test_dir}/Si_cluster_rotated.xyz")
@@ -127,7 +127,7 @@ def generate_Si2O_cluster():
     mol = Molecule.from_sites(struct)
     XYZ(mol).write_file(f"{test_dir}/Si2O_cluster.xyz")
 
-    # Rorate the whole molecule
+    # Rotate the whole molecule
     mol_rotated = mol.copy()
     rotate(mol_rotated, seed=42)
     XYZ(mol_rotated).write_file(f"{test_dir}/Si2O_cluster_rotated.xyz")
@@ -194,8 +194,8 @@ def fit_with_mapper(self, mapper):
         ]
         mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
         op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
-        rotcoords = [op.operate(c) for c in coords]
-        mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
+        rot_coords = [op.operate(c) for c in coords]
+        mol2 = Molecule(["C", "H", "H", "H", "H"], rot_coords)
         mm = MoleculeMatcher(mapper=mapper)
         assert mm.fit(mol1, mol2)
 
@@ -293,10 +293,10 @@ def test_rotated_molecule(self):
         ]
 
         op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
-        rotcoords = [op.operate(c) for c in coords]
+        rot_coords = [op.operate(c) for c in coords]
 
         mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
-        mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
+        mol2 = Molecule(["C", "H", "H", "H", "H"], rot_coords)
 
         mm = KabschMatcher(mol1)
         _, rmsd = mm.fit(mol2)
@@ -368,10 +368,10 @@ def test_rotated_molecule(self):
         ]
 
         op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
-        rotcoords = [op.operate(c) for c in coords]
+        rot_coords = [op.operate(c) for c in coords]
 
         mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
-        mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
+        mol2 = Molecule(["C", "H", "H", "H", "H"], rot_coords)
 
         mm = HungarianOrderMatcher(mol1)
         _, rmsd = mm.fit(mol2)
@@ -473,10 +473,10 @@ def test_rotated_molecule(self):
         ]
 
         op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
-        rotcoords = [op.operate(c) for c in coords]
+        rot_coords = [op.operate(c) for c in coords]
 
         mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
-        mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
+        mol2 = Molecule(["C", "H", "H", "H", "H"], rot_coords)
 
         mm = GeneticOrderMatcher(mol1, threshold=0.3)
         _, rmsd = mm.fit(mol2)[0]