test_remove_oxidation_states() assert struct_out is struct_specie

refactor existing tests to use new return value

pymatgen/analysis/structure_analyzer.py

@@ -518,8 +518,7 @@ def sulfide_type(structure):
     Returns:
         (str) sulfide/polysulfide or None if structure is a sulfate.
     """
-    structure = structure.copy()
-    structure.remove_oxidation_states()
+    structure = structure.copy().remove_oxidation_states()
     sulphur = Element("S")
     comp = structure.composition
     if comp.is_element or sulphur not in comp:

pymatgen/io/cp2k/utils.py

@@ -120,7 +120,7 @@ def atoi(t):
     return [atoi(c) for c in re.split(r"_(\d+)", text)]
 
 
-def get_unique_site_indices(structure: Structure | Molecule):
+def get_unique_site_indices(struct: Structure | Molecule):
     """
     Get unique site indices for a structure according to site properties. Whatever site-property
     has the most unique values is used for indexing.
@@ -147,31 +147,27 @@ def get_unique_site_indices(structure: Structure | Molecule):
         "aux_basis",
     }
 
-    for site in structure:
+    for site in struct:
         for sp in site.species:
             oxi_states.append(getattr(sp, "oxi_state", 0))
             spins.append(getattr(sp, "_properties", {}).get("spin", 0))
 
-    structure.add_site_property("oxi_state", oxi_states)
-    structure.add_site_property("spin", spins)
-    structure.remove_oxidation_states()
+    struct.add_site_property("oxi_state", oxi_states)
+    struct.add_site_property("spin", spins)
+    struct.remove_oxidation_states()
     items = [
         (
             site.species_string,
-            *[
-                structure.site_properties[k][i]
-                for k in structure.site_properties
-                if k.lower() in parsable_site_properties
-            ],
+            *[struct.site_properties[k][i] for k in struct.site_properties if k.lower() in parsable_site_properties],
         )
-        for i, site in enumerate(structure)
+        for i, site in enumerate(struct)
     ]
     unique_itms = list(set(items))
     _sites: dict[tuple, list] = {u: [] for u in unique_itms}
     for i, itm in enumerate(items):
         _sites[itm].append(i)
     sites = {}
-    nums = {s: 1 for s in structure.symbol_set}
+    nums = {s: 1 for s in struct.symbol_set}
     for s in _sites:
         sites[f"{s[0]}_{nums[s[0]]}"] = _sites[s]
         nums[s[0]] += 1

pymatgen/transformations/standard_transformations.py

@@ -181,9 +181,7 @@ def apply_transformation(self, structure):
         Returns:
             Non-oxidation state decorated Structure.
         """
-        struct = structure.copy()
-        struct.remove_oxidation_states()
-        return struct
+        return structure.copy().remove_oxidation_states()
 
     @property
     def inverse(self):
@@ -611,25 +609,25 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
         num_atoms = sum(structure.composition.values())
 
         for output in ewald_m.output_lists:
-            s_copy = struct.copy()
+            struct_copy = struct.copy()
             # do deletions afterwards because they screw up the indices of the
             # structure
             del_indices = []
             for manipulation in output[1]:
                 if manipulation[1] is None:
                     del_indices.append(manipulation[0])
                 else:
-                    s_copy[manipulation[0]] = manipulation[1]
-            s_copy.remove_sites(del_indices)
+                    struct_copy[manipulation[0]] = manipulation[1]
+            struct_copy.remove_sites(del_indices)
 
             if self.no_oxi_states:
-                s_copy.remove_oxidation_states()
+                struct_copy.remove_oxidation_states()
 
             self._all_structures.append(
                 {
                     "energy": output[0],
                     "energy_above_minimum": (output[0] - lowest_energy) / num_atoms,
-                    "structure": s_copy.get_sorted_structure(),
+                    "structure": struct_copy.get_sorted_structure(),
                 }
             )
 

tests/analysis/test_local_env.py

@@ -1226,10 +1226,9 @@ def test_weighted_cn_no_oxid(self):
             3.3897, 3.2589, 3.1207, 3.1924, 3.1915, 3.1207, 3.2598, 3.3897,
         ]
         # fmt: on
-        s = self.lifepo4.copy()
-        s.remove_oxidation_states()
-        for idx in range(len(s)):
-            cn_array.append(cnn.get_cn(s, idx, use_weights=True))
+        struct = self.lifepo4.copy().remove_oxidation_states()
+        for idx in range(len(struct)):
+            cn_array.append(cnn.get_cn(struct, idx, use_weights=True))
 
         assert_allclose(expected_array, cn_array, 2)
 

tests/core/test_structure.py

@@ -1099,10 +1099,11 @@ def test_remove_oxidation_states(self):
         o_specie = Species("O", -2)
         coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
         lattice = Lattice.cubic(10)
-        s_elem = Structure(lattice, [co_elem, o_elem], coords)
-        s_specie = Structure(lattice, [co_specie, o_specie], coords)
-        s_specie.remove_oxidation_states()
-        assert s_elem == s_specie, "Oxidation state remover failed"
+        struct_elem = Structure(lattice, [co_elem, o_elem], coords)
+        struct_specie = Structure(lattice, [co_specie, o_specie], coords)
+        struct_out = struct_specie.remove_oxidation_states()
+        assert struct_out is struct_specie
+        assert struct_elem == struct_specie, "Oxidation state remover failed"
 
     def test_add_oxidation_states_by_guess(self):
         struct = PymatgenTest.get_structure("Li2O")

tests/transformations/test_advanced_transformations.py

@@ -294,8 +294,7 @@ def setUp(self):
         trans = AutoOxiStateDecorationTransformation()
         self.Fe3O4_oxi = trans.apply_transformation(self.Fe3O4)
 
-        self.Li8Fe2NiCoO8 = Structure.from_file(f"{TEST_FILES_DIR}/Li8Fe2NiCoO8.cif")
-        self.Li8Fe2NiCoO8.remove_oxidation_states()
+        self.Li8Fe2NiCoO8 = Structure.from_file(f"{TEST_FILES_DIR}/Li8Fe2NiCoO8.cif").remove_oxidation_states()
 
     def test_apply_transformation(self):
         trans = MagOrderingTransformation({"Fe": 5})