Clean up tests 2

tests/analysis/elasticity/test_elastic.py

@@ -335,11 +335,11 @@ def test_get_effective_ecs(self):
         # Ensure zero strain is same as SOEC
         test_zero = self.exp_cu.get_effective_ecs(np.zeros((3, 3)))
         assert_allclose(test_zero, self.exp_cu[0])
-        s = np.zeros((3, 3))
-        s[0, 0] = 0.02
-        test_2percent = self.exp_cu.get_effective_ecs(s)
+        strain = np.zeros((3, 3))
+        strain[0, 0] = 0.02
+        test_2percent = self.exp_cu.get_effective_ecs(strain)
         diff = test_2percent - test_zero
-        assert_allclose(self.exp_cu[1].einsum_sequence([s]), diff)
+        assert_allclose(self.exp_cu[1].einsum_sequence([strain]), diff)
 
     def test_get_strain_from_stress(self):
         strain = Strain.from_voigt([0.05, 0, 0, 0, 0, 0])

tests/analysis/elasticity/test_stress.py

@@ -36,13 +36,13 @@ def test_properties(self):
         # von_mises
         assert self.symm_stress.von_mises == approx(11.52253878275)
         # piola_kirchoff 1, 2
-        f = Deformation.from_index_amount((0, 1), 0.03)
+        deform = Deformation.from_index_amount((0, 1), 0.03)
         assert_allclose(
-            self.symm_stress.piola_kirchoff_1(f),
+            self.symm_stress.piola_kirchoff_1(deform),
             [[0.4413, 2.29, 2.42], [2.1358, 5.14, 5.07], [2.2679, 5.07, 5.33]],
         )
         assert_allclose(
-            self.symm_stress.piola_kirchoff_2(f),
+            self.symm_stress.piola_kirchoff_2(deform),
             [[0.377226, 2.1358, 2.2679], [2.1358, 5.14, 5.07], [2.2679, 5.07, 5.33]],
         )
         # voigt

tests/analysis/magnetism/test_jahnteller.py

@@ -16,70 +16,70 @@ def setUp(self):
 
     def test_jahn_teller_species_analysis(self):
         # 1 d-shell electron
-        m = self.jt.get_magnitude_of_effect_from_species("Ti3+", "", "oct")
-        assert m == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Ti3+", "", "oct")
+        assert magnitude == "weak"
 
         # 2 d-shell electrons
-        m = self.jt.get_magnitude_of_effect_from_species("Ti2+", "", "oct")
-        assert m == "weak"
-        m = self.jt.get_magnitude_of_effect_from_species("V3+", "", "oct")
-        assert m == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Ti2+", "", "oct")
+        assert magnitude == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("V3+", "", "oct")
+        assert magnitude == "weak"
 
         # 3
-        m = self.jt.get_magnitude_of_effect_from_species("V2+", "", "oct")
-        assert m == "none"
-        m = self.jt.get_magnitude_of_effect_from_species("Cr3+", "", "oct")
-        assert m == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("V2+", "", "oct")
+        assert magnitude == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Cr3+", "", "oct")
+        assert magnitude == "none"
 
         # 4
-        m = self.jt.get_magnitude_of_effect_from_species("Cr2+", "high", "oct")
-        assert m == "strong"
-        m = self.jt.get_magnitude_of_effect_from_species("Cr2+", "low", "oct")
-        assert m == "weak"
-        m = self.jt.get_magnitude_of_effect_from_species("Mn3+", "high", "oct")
-        assert m == "strong"
-        m = self.jt.get_magnitude_of_effect_from_species("Mn3+", "low", "oct")
-        assert m == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Cr2+", "high", "oct")
+        assert magnitude == "strong"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Cr2+", "low", "oct")
+        assert magnitude == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Mn3+", "high", "oct")
+        assert magnitude == "strong"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Mn3+", "low", "oct")
+        assert magnitude == "weak"
 
         # 5
-        m = self.jt.get_magnitude_of_effect_from_species("Mn2+", "high", "oct")
-        assert m == "none"
-        m = self.jt.get_magnitude_of_effect_from_species("Mn2+", "low", "oct")
-        assert m == "weak"
-        m = self.jt.get_magnitude_of_effect_from_species("Fe3+", "high", "oct")
-        assert m == "none"
-        m = self.jt.get_magnitude_of_effect_from_species("Fe3+", "low", "oct")
-        assert m == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Mn2+", "high", "oct")
+        assert magnitude == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Mn2+", "low", "oct")
+        assert magnitude == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Fe3+", "high", "oct")
+        assert magnitude == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Fe3+", "low", "oct")
+        assert magnitude == "weak"
 
         # 6
-        m = self.jt.get_magnitude_of_effect_from_species("Fe2+", "high", "oct")
-        assert m == "weak"
-        m = self.jt.get_magnitude_of_effect_from_species("Fe2+", "low", "oct")
-        assert m == "none"
-        m = self.jt.get_magnitude_of_effect_from_species("Co3+", "high", "oct")
-        assert m == "weak"
-        m = self.jt.get_magnitude_of_effect_from_species("Co3+", "low", "oct")
-        assert m == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Fe2+", "high", "oct")
+        assert magnitude == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Fe2+", "low", "oct")
+        assert magnitude == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Co3+", "high", "oct")
+        assert magnitude == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Co3+", "low", "oct")
+        assert magnitude == "none"
 
         # 7
-        m = self.jt.get_magnitude_of_effect_from_species("Co2+", "high", "oct")
-        assert m == "weak"
-        m = self.jt.get_magnitude_of_effect_from_species("Co2+", "low", "oct")
-        assert m == "strong"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Co2+", "high", "oct")
+        assert magnitude == "weak"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Co2+", "low", "oct")
+        assert magnitude == "strong"
 
         # 8
-        m = self.jt.get_magnitude_of_effect_from_species("Ni2+", "", "oct")
-        assert m == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Ni2+", "", "oct")
+        assert magnitude == "none"
 
         # 9
-        m = self.jt.get_magnitude_of_effect_from_species("Cu2+", "", "oct")
-        assert m == "strong"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Cu2+", "", "oct")
+        assert magnitude == "strong"
 
         # 10
-        m = self.jt.get_magnitude_of_effect_from_species("Cu+", "", "oct")
-        assert m == "none"
-        m = self.jt.get_magnitude_of_effect_from_species("Zn2+", "", "oct")
-        assert m == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Cu+", "", "oct")
+        assert magnitude == "none"
+        magnitude = self.jt.get_magnitude_of_effect_from_species("Zn2+", "", "oct")
+        assert magnitude == "none"
 
     def test_jahn_teller_structure_analysis(self):
         LiFePO4 = Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif", primitive=True)

tests/analysis/structure_prediction/test_substitutor.py

@@ -20,19 +20,19 @@ def get_table():
 
 class TestSubstitutor(PymatgenTest):
     def setUp(self):
-        self.s = Substitutor(threshold=1e-3, lambda_table=get_table(), alpha=-5.0)
+        self.substitutor = Substitutor(threshold=1e-3, lambda_table=get_table(), alpha=-5.0)
 
     def test_substitutor(self):
         s_list = [Species("O", -2), Species("Li", 1)]
-        subs = self.s.pred_from_list(s_list)
+        subs = self.substitutor.pred_from_list(s_list)
         assert len(subs) == 4, "incorrect number of substitutions"
         comp = Composition({"O2-": 1, "Li1+": 2})
-        subs = self.s.pred_from_comp(comp)
+        subs = self.substitutor.pred_from_comp(comp)
         assert len(subs) == 4, "incorrect number of substitutions"
 
         structures = [{"structure": PymatgenTest.get_structure("Li2O"), "id": "pmgtest"}]
-        subs = self.s.pred_from_structures(["Na+", "O2-"], structures)
+        subs = self.substitutor.pred_from_structures(["Na+", "O2-"], structures)
         assert subs[0].formula == "Na2 O1"
 
     def test_as_dict(self):
-        Substitutor.from_dict(self.s.as_dict())
+        Substitutor.from_dict(self.substitutor.as_dict())

tests/analysis/structure_prediction/test_volume_predictor.py

@@ -18,49 +18,49 @@ def test_predict(self):
         nacl = PymatgenTest.get_structure("CsCl")
         nacl.replace_species({"Cs": "Na"})
         nacl.scale_lattice(184.384551033)
-        p = RLSVolumePredictor(radii_type="ionic")
-        assert p.predict(struct, nacl) == approx(342.84905395082535)
-        p = RLSVolumePredictor(radii_type="atomic")
-        assert p.predict(struct, nacl) == approx(391.884366481)
+        predictor = RLSVolumePredictor(radii_type="ionic")
+        assert predictor.predict(struct, nacl) == approx(342.84905395082535)
+        predictor = RLSVolumePredictor(radii_type="atomic")
+        assert predictor.predict(struct, nacl) == approx(391.884366481)
         lif = PymatgenTest.get_structure("CsCl")
         lif.replace_species({"Cs": "Li", "Cl": "F"})
-        p = RLSVolumePredictor(radii_type="ionic")
-        assert p.predict(lif, nacl) == approx(74.268402413690467)
-        p = RLSVolumePredictor(radii_type="atomic")
-        assert p.predict(lif, nacl) == approx(62.2808125839)
+        predictor = RLSVolumePredictor(radii_type="ionic")
+        assert predictor.predict(lif, nacl) == approx(74.268402413690467)
+        predictor = RLSVolumePredictor(radii_type="atomic")
+        assert predictor.predict(lif, nacl) == approx(62.2808125839)
 
         lfpo = PymatgenTest.get_structure("LiFePO4")
         lmpo = PymatgenTest.get_structure("LiFePO4")
         lmpo.replace_species({"Fe": "Mn"})
-        p = RLSVolumePredictor(radii_type="ionic")
-        assert p.predict(lmpo, lfpo) == approx(310.08253254420134)
-        p = RLSVolumePredictor(radii_type="atomic")
-        assert p.predict(lmpo, lfpo) == approx(299.607967711)
+        predictor = RLSVolumePredictor(radii_type="ionic")
+        assert predictor.predict(lmpo, lfpo) == approx(310.08253254420134)
+        predictor = RLSVolumePredictor(radii_type="atomic")
+        assert predictor.predict(lmpo, lfpo) == approx(299.607967711)
 
         sto = PymatgenTest.get_structure("SrTiO3")
         scoo = PymatgenTest.get_structure("SrTiO3")
         scoo.replace_species({"Ti4+": "Co4+"})
-        p = RLSVolumePredictor(radii_type="ionic")
-        assert p.predict(scoo, sto) == approx(56.162534974936463)
-        p = RLSVolumePredictor(radii_type="atomic")
-        assert p.predict(scoo, sto) == approx(57.4777835108)
+        predictor = RLSVolumePredictor(radii_type="ionic")
+        assert predictor.predict(scoo, sto) == approx(56.162534974936463)
+        predictor = RLSVolumePredictor(radii_type="atomic")
+        assert predictor.predict(scoo, sto) == approx(57.4777835108)
 
         # Use Ag7P3S11 as a test case:
 
         # (i) no oxidation states are assigned and CVP-atomic scheme is selected.
         aps = Structure.from_file(f"{module_dir}/Ag7P3S11_mp-683910_primitive.cif")
         apo = Structure.from_file(f"{module_dir}/Ag7P3S11_mp-683910_primitive.cif")
         apo.replace_species({"S": "O"})
-        p = RLSVolumePredictor(radii_type="atomic", check_isostructural=False)
-        assert p.predict(apo, aps) == approx(1196.31384276)
+        predictor = RLSVolumePredictor(radii_type="atomic", check_isostructural=False)
+        assert predictor.predict(apo, aps) == approx(1196.31384276)
 
         # (ii) Oxidation states are assigned.
         apo.add_oxidation_state_by_element({"Ag": 1, "P": 5, "O": -2})
         aps.add_oxidation_state_by_element({"Ag": 1, "P": 5, "S": -2})
-        p = RLSVolumePredictor(radii_type="ionic")
-        assert p.predict(apo, aps) == approx(1165.23259079)
-        p = RLSVolumePredictor(radii_type="atomic")
-        assert p.predict(apo, aps) == approx(1196.31384276)
+        predictor = RLSVolumePredictor(radii_type="ionic")
+        assert predictor.predict(apo, aps) == approx(1165.23259079)
+        predictor = RLSVolumePredictor(radii_type="atomic")
+        assert predictor.predict(apo, aps) == approx(1196.31384276)
 
     def test_modes(self):
         cs_cl = PymatgenTest.get_structure("CsCl")

tests/analysis/test_adsorption.py

@@ -117,9 +117,9 @@ def test_generate_adsorption_structures(self):
 
     def test_adsorb_both_surfaces(self):
         # Test out for monatomic adsorption
-        o = Molecule("O", [[0, 0, 0]])
-        ad_slabs = self.asf_100.adsorb_both_surfaces(o)
-        ad_slabs_one = self.asf_100.generate_adsorption_structures(o)
+        oxi = Molecule("O", [[0, 0, 0]])
+        ad_slabs = self.asf_100.adsorb_both_surfaces(oxi)
+        ad_slabs_one = self.asf_100.generate_adsorption_structures(oxi)
         assert len(ad_slabs) == len(ad_slabs_one)
         for ad_slab in ad_slabs:
             sg = SpacegroupAnalyzer(ad_slab)

tests/analysis/test_dimensionality.py

@@ -107,8 +107,8 @@ def test_zero_d_to_molecule_graph(self):
             zero_d_graph_to_molecule_graph(self.graphite, comp_graphs[0])
 
         # test for a troublesome structure
-        s = loadfn(f"{TEST_FILES_DIR}/PH7CN3O3F.json.gz")
-        bs = CrystalNN().get_bonded_structure(s)
+        struct = loadfn(f"{TEST_FILES_DIR}/PH7CN3O3F.json.gz")
+        bs = CrystalNN().get_bonded_structure(struct)
         comp_graphs = [bs.graph.subgraph(c) for c in nx.weakly_connected_components(bs.graph)]
         mol_graph = zero_d_graph_to_molecule_graph(bs, comp_graphs[0])
         assert len(mol_graph.molecule) == 12

tests/analysis/test_energy_models.py

@@ -26,11 +26,11 @@ def test_get_energy(self):
             coords,
         )
 
-        m = EwaldElectrostaticModel()
+        model = EwaldElectrostaticModel()
         # large tolerance because scipy constants changed between 0.16.1 and 0.17
-        assert m.get_energy(struct) == approx(-264.66364858, abs=1e-2)  # Result from GULP
+        assert model.get_energy(struct) == approx(-264.66364858, abs=1e-2)  # Result from GULP
         s2 = Structure.from_file(f"{TEST_FILES_DIR}/Li2O.cif")
-        assert m.get_energy(s2) == approx(-145.39050015844839, abs=1e-4)
+        assert model.get_energy(s2) == approx(-145.39050015844839, abs=1e-4)
 
     def test_as_from_dict(self):
         model = EwaldElectrostaticModel()

tests/analysis/test_ewald.py

@@ -109,11 +109,11 @@ def test_site(self):
         """Test that uses an uncharged structure."""
         filepath = f"{VASP_IN_DIR}/POSCAR"
         struct = Structure.from_file(filepath)
-        s = struct.copy()
-        s.add_oxidation_state_by_element({"Li": 1, "Fe": 3, "P": 5, "O": -2})
+        struct = struct.copy()
+        struct.add_oxidation_state_by_element({"Li": 1, "Fe": 3, "P": 5, "O": -2})
 
         # Comparison to LAMMPS result
-        ham = EwaldSummation(s, compute_forces=True)
+        ham = EwaldSummation(struct, compute_forces=True)
         assert approx(ham.total_energy, abs=1e-3) == -1226.3335
         assert approx(ham.get_site_energy(0), abs=1e-3) == -45.8338
         assert approx(ham.get_site_energy(8), abs=1e-3) == -27.2978

tests/analysis/test_phase_diagram.py

@@ -489,8 +489,8 @@ def test_get_hull_energy_per_atom(self):
     def test_1d_pd(self):
         entry = PDEntry("H", 0)
         pd = PhaseDiagram([entry])
-        decomp, e = pd.get_decomp_and_e_above_hull(PDEntry("H", 1))
-        assert e == 1
+        decomp, e_above_hull = pd.get_decomp_and_e_above_hull(PDEntry("H", 1))
+        assert e_above_hull == 1
         assert decomp[entry] == approx(1.0)
 
     def test_get_critical_compositions_fractional(self):