global replace get_structure

tests/alchemy/test_materials.py

@@ -16,14 +16,14 @@
     SupercellTransformation,
 )
 from pymatgen.util.provenance import StructureNL
-from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, MatSciTest
 
 TEST_DIR = f"{TEST_FILES_DIR}/alchemy"
 
 
 class TestTransformedStructure(MatSciTest):
     def setup_method(self):
-        structure = PymatgenTest.get_structure("LiFePO4")
+        structure = MatSciTest.get_structure("LiFePO4")
         self.structure = structure
         trafos = [SubstitutionTransformation({"Li": "Na"})]
         self.trans = TransformedStructure(structure, trafos)

tests/alchemy/test_transmuters.py

@@ -8,7 +8,7 @@
     RemoveSpeciesTransformation,
     SubstitutionTransformation,
 )
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, MatSciTest
 
 
 class TestCifTransmuter(MatSciTest):

tests/analysis/structure_prediction/test_substitutor.py

@@ -4,7 +4,7 @@
 
 from pymatgen.analysis.structure_prediction.substitutor import Substitutor
 from pymatgen.core import Composition, Species
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, MatSciTest
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/struct_predictor"
 
@@ -32,7 +32,7 @@ def test_substitutor(self):
         subs = self.substitutor.pred_from_comp(comp)
         assert len(subs) == 4, "incorrect number of substitutions"
 
-        structures = [{"structure": PymatgenTest.get_structure("Li2O"), "id": "pmgtest"}]
+        structures = [{"structure": MatSciTest.get_structure("Li2O"), "id": "pmgtest"}]
         subs = self.substitutor.pred_from_structures(["Na+", "O2-"], structures)
         assert subs[0].formula == "Na2 O1"
 

tests/analysis/structure_prediction/test_volume_predictor.py

@@ -5,38 +5,38 @@
 
 from pymatgen.analysis.structure_prediction.volume_predictor import DLSVolumePredictor, RLSVolumePredictor
 from pymatgen.core import Structure
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, MatSciTest
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/structure_prediction"
 
 
 class TestRLSVolumePredictor(MatSciTest):
     def test_predict(self):
-        struct = PymatgenTest.get_structure("CsCl")
-        nacl = PymatgenTest.get_structure("CsCl")
+        struct = MatSciTest.get_structure("CsCl")
+        nacl = MatSciTest.get_structure("CsCl")
         nacl.replace_species({"Cs": "Na"})
         nacl.scale_lattice(184.384551033)
         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 = MatSciTest.get_structure("CsCl")
         lif.replace_species({"Cs": "Li", "Cl": "F"})
         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")
+        lfpo = MatSciTest.get_structure("LiFePO4")
+        lmpo = MatSciTest.get_structure("LiFePO4")
         lmpo.replace_species({"Fe": "Mn"})
         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")
+        sto = MatSciTest.get_structure("SrTiO3")
+        scoo = MatSciTest.get_structure("SrTiO3")
         scoo.replace_species({"Ti4+": "Co4+"})
         predictor = RLSVolumePredictor(radii_type="ionic")
         assert predictor.predict(scoo, sto) == approx(56.162534974936463)
@@ -61,8 +61,8 @@ def test_predict(self):
         assert predictor.predict(apo, aps) == approx(1196.31384276)
 
     def test_modes(self):
-        cs_cl = PymatgenTest.get_structure("CsCl")
-        na_cl = PymatgenTest.get_structure("CsCl")
+        cs_cl = MatSciTest.get_structure("CsCl")
+        na_cl = MatSciTest.get_structure("CsCl")
         na_cl.replace_species({"Cs": "Na"})
         na_cl.scale_lattice(184.384551033)
         vol_pred = RLSVolumePredictor(radii_type="ionic", use_bv=False)
@@ -94,7 +94,7 @@ def test_predict(self):
         assert vol_pred.predict(fen) == approx(fen.volume * 1.5)
         assert p_fast.predict(fen) == approx(fen.volume * 1.5)
 
-        lfpo = PymatgenTest.get_structure("LiFePO4")
+        lfpo = MatSciTest.get_structure("LiFePO4")
 
         lfpo.scale_lattice(lfpo.volume * 3.0)
         assert p_nolimit.predict(lfpo) == approx(291.62094410192924)
@@ -104,6 +104,6 @@ def test_predict(self):
         assert vol_pred.predict(lfpo) == approx(lfpo.volume * 1.5)
         assert p_fast.predict(lfpo) == approx(lfpo.volume * 1.5)
 
-        lmpo = PymatgenTest.get_structure("LiFePO4")
+        lmpo = MatSciTest.get_structure("LiFePO4")
         lmpo.replace_species({"Fe": "Mn"})
         assert vol_pred.predict(lmpo) == approx(290.795329052)

tests/core/test_structure.py

@@ -30,7 +30,7 @@
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.cif import CifParser
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, MatSciTest
 
 try:
     from ase.atoms import Atoms
@@ -46,7 +46,7 @@
 
 class TestNeighbor(MatSciTest):
     def test_msonable(self):
-        struct = PymatgenTest.get_structure("Li2O")
+        struct = MatSciTest.get_structure("Li2O")
         nn = struct.get_neighbors(struct[0], r=3)
         assert isinstance(nn[0], PeriodicNeighbor)
         str_ = json.dumps(nn, cls=MontyEncoder)
@@ -1024,7 +1024,7 @@ def test_mutable_sequence_methods(self):
         assert struct.formula == "Mn1"
 
         # Test slice replacement.
-        struct = PymatgenTest.get_structure("Li2O")
+        struct = MatSciTest.get_structure("Li2O")
         struct[:2] = "S"
         assert struct.formula == "Li1 S2"
 
@@ -1267,7 +1267,7 @@ def test_remove_oxidation_states(self):
         assert struct_elem == struct_specie, "Oxidation state remover failed"
 
     def test_add_oxidation_state_by_guess(self):
-        struct = PymatgenTest.get_structure("Li2O")
+        struct = MatSciTest.get_structure("Li2O")
         returned = struct.add_oxidation_state_by_guess()
         assert returned is struct
         expected = [Species("Li", 1), Species("O", -2)]

tests/io/test_phonopy.py

@@ -28,7 +28,7 @@
     get_pmg_structure,
     get_thermal_displacement_matrices,
 )
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, MatSciTest
 
 try:
     from phonopy import Phonopy
@@ -99,7 +99,7 @@ def test_get_complete_dos(self):
 @pytest.mark.skipif(Phonopy is None, reason="Phonopy not present")
 class TestStructureConversion(MatSciTest):
     def test_structure_conversion(self):
-        struct_pmg = PymatgenTest.get_structure("LiFePO4")
+        struct_pmg = MatSciTest.get_structure("LiFePO4")
         # add magmoms to site_properties
         struct_pmg.add_site_property("magmom", magmoms := [1] * len(struct_pmg))
         struct_ph = get_phonopy_structure(struct_pmg)

tests/io/vasp/test_sets.py

@@ -54,7 +54,7 @@
     get_valid_magmom_struct,
 )
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, MatSciTest
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/vasp"
 
@@ -1501,7 +1501,7 @@ def test_incar(self):
 class TestMVLGWSet(MatSciTest):
     def setup_method(self):
         self.set = MVLGWSet
-        self.struct = PymatgenTest.get_structure("Li2O")
+        self.struct = MatSciTest.get_structure("Li2O")
 
     def test_static(self):
         assert self.set.mode == "STATIC"
@@ -1675,7 +1675,7 @@ def test_init(self):
         assert vis.reciprocal_density == 100
 
         with pytest.warns(BadInputSetWarning, match=r"Hybrid functionals"):
-            vis = self.set(PymatgenTest.get_structure("Li2O"), user_incar_settings={"ALGO": "Fast"})
+            vis = self.set(MatSciTest.get_structure("Li2O"), user_incar_settings={"ALGO": "Fast"})
             vis.incar.items()
 
     def test_override_from_prev_calc(self):
@@ -1991,7 +1991,7 @@ def test_override_from_prev_calc(self):
 class TestFunc(MatSciTest):
     @skip_if_no_psp_dir
     def test_batch_write_input(self):
-        structs = list(map(PymatgenTest.get_structure, ("Li2O", "LiFePO4")))
+        structs = list(map(MatSciTest.get_structure, ("Li2O", "LiFePO4")))
 
         batch_write_input(structs, sanitize=True)
         for formula in ("Li4Fe4P4O16_1", "Li2O1_0"):

tests/symmetry/test_analyzer.py

@@ -18,7 +18,7 @@
     iterative_symmetrize,
 )
 from pymatgen.symmetry.structure import SymmetrizedStructure
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, MatSciTest
 
 TEST_DIR = f"{TEST_FILES_DIR}/symmetry/analyzer"
 
@@ -54,7 +54,7 @@ def test_is_laue(self):
         assert self.disordered_sg.is_laue()
 
     def test_magnetic(self):
-        lfp = PymatgenTest.get_structure("LiFePO4")
+        lfp = MatSciTest.get_structure("LiFePO4")
         sg = SpacegroupAnalyzer(lfp, 0.1)
         assert sg.get_space_group_symbol() == "Pnma"
         magmoms = [0] * len(lfp)
@@ -670,7 +670,7 @@ def test_symmetrize_molecule2(self):
 
     def test_get_kpoint_weights(self):
         for name in ("SrTiO3", "LiFePO4", "Graphite"):
-            struct = PymatgenTest.get_structure(name)
+            struct = MatSciTest.get_structure(name)
             spga = SpacegroupAnalyzer(struct)
             ir_mesh = spga.get_ir_reciprocal_mesh((4, 4, 4))
             weights = [i[1] for i in ir_mesh]
@@ -679,7 +679,7 @@ def test_get_kpoint_weights(self):
                 assert weight == approx(expected)
 
         for name in ("SrTiO3", "LiFePO4", "Graphite"):
-            struct = PymatgenTest.get_structure(name)
+            struct = MatSciTest.get_structure(name)
             spga = SpacegroupAnalyzer(struct)
             ir_mesh = spga.get_ir_reciprocal_mesh((1, 2, 3))
             weights = [i[1] for i in ir_mesh]

tests/transformations/test_advanced_transformations.py

@@ -40,7 +40,7 @@
     OxidationStateDecorationTransformation,
     SubstitutionTransformation,
 )
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, MatSciTest
 
 try:
     import hiphive
@@ -490,7 +490,7 @@ def test_advanced_usage(self):
 @pytest.mark.skipif(not enumlib_present, reason="enum_lib not present.")
 class TestDopingTransformation(MatSciTest):
     def test_apply_transformation(self):
-        structure = PymatgenTest.get_structure("LiFePO4")
+        structure = MatSciTest.get_structure("LiFePO4")
         spga = SpacegroupAnalyzer(structure, 0.1)
         structure = spga.get_refined_structure()
         trafo = DopingTransformation("Ca2+", min_length=10)
@@ -524,7 +524,7 @@ def test_apply_transformation(self):
                 assert d["structure"].charge == 0
 
         # Make sure compensation is done with lowest oxi state
-        structure = PymatgenTest.get_structure("SrTiO3")
+        structure = MatSciTest.get_structure("SrTiO3")
         trafo = DopingTransformation(
             "Nb5+",
             min_length=5,