fix alchemy and anlysis

tests/alchemy/test_filters.py

@@ -72,7 +72,7 @@ def test_as_from_dict(self):
 
 class TestRemoveDuplicatesFilter(TestCase):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json") as file:
+        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json", encoding="utf-8") as file:
             entries = json.load(file, cls=MontyDecoder)
         self._struct_list = [entry.structure for entry in entries]
         self._sm = StructureMatcher()
@@ -91,7 +91,7 @@ def test_as_from_dict(self):
 
 class TestRemoveExistingFilter(TestCase):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json") as file:
+        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json", encoding="utf-8") as file:
             entries = json.load(file, cls=MontyDecoder)
         self._struct_list = [entry.structure for entry in entries]
         self._sm = StructureMatcher()

tests/alchemy/test_materials.py

@@ -64,7 +64,7 @@ def test_final_structure(self):
         assert isinstance(deepcopy(self.trans), TransformedStructure)
 
     def test_from_dict(self):
-        with open(f"{TEST_DIR}/transformations.json") as file:
+        with open(f"{TEST_DIR}/transformations.json", encoding="utf-8") as file:
             dct = json.load(file)
         dct["other_parameters"] = {"tags": ["test"]}
         t_struct = TransformedStructure.from_dict(dct)

tests/analysis/chemenv/connectivity/test_connected_components.py

@@ -838,7 +838,7 @@ def test_real_systems(self):
 
     def test_coordination_sequences(self):
         BaTiO3_se_fpath = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments/se_mp-5020.json"
-        with open(BaTiO3_se_fpath) as file:
+        with open(BaTiO3_se_fpath, encoding="utf-8") as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)
         lse = LightStructureEnvironments.from_structure_environments(

tests/analysis/chemenv/connectivity/test_structure_connectivity.py

@@ -17,7 +17,7 @@
 class TestStructureConnectivity(PymatgenTest):
     def test_serialization(self):
         BaTiO3_se_fpath = f"{TEST_FILES_DIR}/analysis/chemenv/structure_environments/se_mp-5020.json"
-        with open(BaTiO3_se_fpath) as file:
+        with open(BaTiO3_se_fpath, encoding="utf-8") as file:
             dd = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dd)
         lse = LightStructureEnvironments.from_structure_environments(

tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py

@@ -142,7 +142,7 @@ def _strategy_test(self, strategy):
 
         for json_file in files:
             with self.subTest(json_file=json_file):
-                with open(f"{json_dir}/{json_file}") as file:
+                with open(f"{json_dir}/{json_file}", encoding="utf-8") as file:
                     dct = json.load(file)
 
                 atom_indices = dct["atom_indices"]

tests/analysis/chemenv/coordination_environments/test_read_write.py

@@ -37,7 +37,7 @@ def setUpClass(cls):
         cls.lgf.setup_parameters(centering_type="standard")
 
     def test_read_write_structure_environments(self):
-        with open(f"{json_dir}/test_T--4_FePO4_icsd_4266.json") as file:
+        with open(f"{json_dir}/test_T--4_FePO4_icsd_4266.json", encoding="utf-8") as file:
             dd = json.load(file)
 
         atom_indices = dd["atom_indices"]
@@ -51,7 +51,7 @@ def test_read_write_structure_environments(self):
         with open(f"{self.tmp_path}/se.json", mode="w") as file:
             json.dump(se.as_dict(), file)
 
-        with open(f"{self.tmp_path}/se.json") as file:
+        with open(f"{self.tmp_path}/se.json", encoding="utf-8") as file:
             dd = json.load(file)
 
         se2 = StructureEnvironments.from_dict(dd)
@@ -70,13 +70,13 @@ def test_read_write_structure_environments(self):
                 default=lambda obj: getattr(obj, "tolist", lambda: obj)(),
             )
 
-        with open(f"{self.tmp_path}/lse.json") as file:
+        with open(f"{self.tmp_path}/lse.json", encoding="utf-8") as file:
             LightStructureEnvironments.from_dict(json.load(file))
 
         # assert lse == lse2
 
     def test_structure_environments_neighbors_sets(self):
-        with open(f"{struct_env_dir}/se_mp-7000.json") as file:
+        with open(f"{struct_env_dir}/se_mp-7000.json", encoding="utf-8") as file:
             dct = json.load(file)
 
         struct_envs = StructureEnvironments.from_dict(dct)
@@ -221,7 +221,7 @@ def test_strategies(self):
         assert multi_weights_strategy_2 != multi_weights_strategy_3
 
     def test_read_write_voronoi(self):
-        with open(f"{json_dir}/test_T--4_FePO4_icsd_4266.json") as file:
+        with open(f"{json_dir}/test_T--4_FePO4_icsd_4266.json", encoding="utf-8") as file:
             dd = json.load(file)
 
         struct = Structure.from_dict(dd["structure"])
@@ -230,10 +230,10 @@ def test_read_write_voronoi(self):
 
         detailed_voronoi_container = DetailedVoronoiContainer(structure=struct, valences=valences)
 
-        with open(f"{self.tmp_path}/se.json", mode="w") as file:
+        with open(f"{self.tmp_path}/se.json", mode="w", encoding="utf-8") as file:
             json.dump(detailed_voronoi_container.as_dict(), file)
 
-        with open(f"{self.tmp_path}/se.json") as file:
+        with open(f"{self.tmp_path}/se.json", encoding="utf-8") as file:
             dd = json.load(file)
 
         detailed_voronoi_container2 = DetailedVoronoiContainer.from_dict(dd)

tests/analysis/chemenv/coordination_environments/test_structure_environments.py

@@ -26,7 +26,7 @@
 
 class TestStructureEnvironments(PymatgenTest):
     def test_structure_environments(self):
-        with open(f"{TEST_DIR}/se_mp-7000.json") as file:
+        with open(f"{TEST_DIR}/se_mp-7000.json", encoding="utf-8") as file:
             dct = json.load(file)
 
         struct_envs = StructureEnvironments.from_dict(dct)
@@ -143,7 +143,7 @@ def test_structure_environments(self):
         assert ce != ce2
 
     def test_light_structure_environments(self):
-        with open(f"{TEST_DIR}/se_mp-7000.json") as file:
+        with open(f"{TEST_DIR}/se_mp-7000.json", encoding="utf-8") as file:
             dct = json.load(file)
 
         struct_envs = StructureEnvironments.from_dict(dct)

tests/analysis/chemenv/coordination_environments/test_weights.py

@@ -240,7 +240,7 @@ def test_CN_bias_weight(self):
 
     def test_self_csms_weight(self):
         # Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
-        with open(f"{struct_env_dir}/se_mp-743972.json") as file:
+        with open(f"{struct_env_dir}/se_mp-743972.json", encoding="utf-8") as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)
 
@@ -316,7 +316,7 @@ def test_self_csms_weight(self):
         assert abs(self_w - 0.14204073172729198) < 1e-8
 
         # Get the StructureEnvironments for SiO2 (mp-7000)
-        with open(f"{struct_env_dir}/se_mp-7000.json") as file:
+        with open(f"{struct_env_dir}/se_mp-7000.json", encoding="utf-8") as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)
 
@@ -360,7 +360,7 @@ def test_self_csms_weight(self):
 
     def test_delta_csms_weight(self):
         # Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
-        with open(f"{struct_env_dir}/se_mp-743972.json") as file:
+        with open(f"{struct_env_dir}/se_mp-743972.json", encoding="utf-8") as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)
 
@@ -492,7 +492,7 @@ def test_delta_csms_weight(self):
         assert abs(delta_w - 0.103515625) < 1e-8
 
         # Get the StructureEnvironments for SiO2 (mp-7000)
-        with open(f"{struct_env_dir}/se_mp-7000.json") as file:
+        with open(f"{struct_env_dir}/se_mp-7000.json", encoding="utf-8") as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)
 

tests/analysis/elasticity/test_elastic.py

@@ -67,9 +67,9 @@ def setUp(self):
 
         self.elastic_tensor_1 = ElasticTensor(self.ft)
         filepath = f"{TEST_DIR}/Sn_def_stress.json"
-        with open(filepath) as file:
+        with open(filepath, encoding="utf-8") as file:
             self.def_stress_dict = json.load(file)
-        with open(f"{TEST_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json", encoding="utf-8") as file:
             self.toec_dict = json.load(file)
         self.structure = self.get_structure("Sn")
 
@@ -265,7 +265,7 @@ def test_energy_density(self):
 
 class TestElasticTensorExpansion(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json", encoding="utf-8") as file:
             self.data_dict = json.load(file)
         self.strains = [Strain(sm) for sm in self.data_dict["strains"]]
         self.pk_stresses = [Stress(d) for d in self.data_dict["pk_stresses"]]
@@ -366,7 +366,7 @@ def test_get_yield_stress(self):
 
 class TestNthOrderElasticTensor(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json", encoding="utf-8") as file:
             self.data_dict = json.load(file)
         self.strains = [Strain(sm) for sm in self.data_dict["strains"]]
         self.pk_stresses = [Stress(d) for d in self.data_dict["pk_stresses"]]
@@ -405,7 +405,7 @@ class TestDiffFit(PymatgenTest):
     """Test various functions related to diff fitting."""
 
     def setUp(self):
-        with open(f"{TEST_DIR}/test_toec_data.json") as file:
+        with open(f"{TEST_DIR}/test_toec_data.json", encoding="utf-8") as file:
             self.data_dict = json.load(file)
         self.strains = [Strain(sm) for sm in self.data_dict["strains"]]
         self.pk_stresses = [Stress(d) for d in self.data_dict["pk_stresses"]]

tests/analysis/structure_prediction/test_substitution_probability.py

@@ -22,7 +22,7 @@ def get_table():
     default lambda table.
     """
     json_path = f"{TEST_DIR}/test_lambda.json"
-    with open(json_path) as file:
+    with open(json_path, encoding="utf-8") as file:
         return json.load(file)
 
 

tests/analysis/structure_prediction/test_substitutor.py

@@ -16,7 +16,7 @@ def get_table():
     default lambda table.
     """
     json_path = f"{TEST_DIR}/test_lambda.json"
-    with open(json_path) as file:
+    with open(json_path, encoding="utf-8") as file:
         return json.load(file)
 
 

tests/analysis/test_graphs.py

@@ -86,7 +86,7 @@ def setUp(self):
         # MoS2 example, structure graph obtained from critic2
         # (not ground state, from mp-1023924, single layer)
         stdout_file = f"{TEST_FILES_DIR}/command_line/critic2/MoS2_critic2_stdout.txt"
-        with open(stdout_file) as txt_file:
+        with open(stdout_file, encoding="utf-8") as txt_file:
             reference_stdout = txt_file.read()
         self.structure = Structure.from_file(f"{TEST_FILES_DIR}/command_line/critic2/MoS2.cif")
         c2o = Critic2Analysis(self.structure, reference_stdout)

tests/analysis/test_molecule_matcher.py

@@ -164,12 +164,12 @@ def test_get_rmsd(self):
     @pytest.mark.skipif(platform.system() == "Windows", reason="Tests for openbabel failing on Win")
     def test_group_molecules(self):
         mol_matcher = MoleculeMatcher(tolerance=0.001)
-        with open(f"{TEST_DIR}/mol_list.txt") as file:
+        with open(f"{TEST_DIR}/mol_list.txt", encoding="utf-8") as file:
             filename_list = [line.strip() for line in file]
         mol_list = [Molecule.from_file(f"{TEST_DIR}/{file}") for file in filename_list]
         mol_groups = mol_matcher.group_molecules(mol_list)
         filename_groups = [[filename_list[mol_list.index(m)] for m in g] for g in mol_groups]
-        with open(f"{TEST_DIR}/grouped_mol_list.txt") as file:
+        with open(f"{TEST_DIR}/grouped_mol_list.txt", encoding="utf-8") as file:
             grouped_text = file.read().strip()
         assert str(filename_groups) == grouped_text
 

tests/analysis/test_structure_matcher.py

@@ -24,7 +24,7 @@
 
 class TestStructureMatcher(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json") as file:
+        with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json", encoding="utf-8") as file:
             entries = json.load(file, cls=MontyDecoder)
         self.struct_list = [ent.structure for ent in entries]
         self.oxi_structs = [

tests/analysis/test_surface_analysis.py

@@ -24,7 +24,7 @@
 
 class TestSlabEntry(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_DIR}/ucell_entries.txt") as file:
+        with open(f"{TEST_DIR}/ucell_entries.txt", encoding="utf-8") as file:
             ucell_entries = json.loads(file.read())
         self.ucell_entries = ucell_entries
 
@@ -58,7 +58,7 @@ def test_properties(self):
                         assert ads.Nsurfs_ads_in_slab == 1
 
                         # Determine the correct binding energy
-                        with open(f"{TEST_DIR}/isolated_O_entry.txt") as txt_file:
+                        with open(f"{TEST_DIR}/isolated_O_entry.txt", encoding="utf-8") as txt_file:
                             isolated_O_entry = json.loads(txt_file.read())
                         O_cse = ComputedStructureEntry.from_dict(isolated_O_entry)
                         g_bind = (ads.energy - ml * clean.energy) / Nads - O_cse.energy_per_atom
@@ -122,7 +122,7 @@ class TestSurfaceEnergyPlotter(PymatgenTest):
     def setUp(self):
         entry_dict = get_entry_dict(f"{TEST_DIR}/Cu_entries.txt")
         self.Cu_entry_dict = entry_dict
-        with open(f"{TEST_DIR}/ucell_entries.txt") as file:
+        with open(f"{TEST_DIR}/ucell_entries.txt", encoding="utf-8") as file:
             ucell_entries = json.loads(file.read())
 
         self.Cu_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Cu"])
@@ -314,7 +314,7 @@ def setUp(self):
         # Load all entries
         La_hcp_entry_dict = get_entry_dict(f"{TEST_DIR}/La_hcp_entries.txt")
         La_fcc_entry_dict = get_entry_dict(f"{TEST_DIR}/La_fcc_entries.txt")
-        with open(f"{TEST_DIR}/ucell_entries.txt") as txt_file:
+        with open(f"{TEST_DIR}/ucell_entries.txt", encoding="utf-8") as txt_file:
             ucell_entries = json.loads(txt_file.read())
         La_hcp_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["La_hcp"])
         La_fcc_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["La_fcc"])
@@ -365,7 +365,7 @@ def get_entry_dict(filename):
     # helper to generate an entry_dict
 
     entry_dict = {}
-    with open(filename) as file:
+    with open(filename, encoding="utf-8") as file:
         entries = json.loads(file.read())
     for entry in entries:
         sub_str = entry[25:]
@@ -392,7 +392,7 @@ def load_O_adsorption():
     # Loads the dictionary for clean and O adsorbed Rh, Pt, and Ni entries
 
     # Load the adsorbate as an entry
-    with open(f"{TEST_DIR}/isolated_O_entry.txt") as file:
+    with open(f"{TEST_DIR}/isolated_O_entry.txt", encoding="utf-8") as file:
         isolated_O_entry = json.loads(file.read())
     O_entry = ComputedStructureEntry.from_dict(isolated_O_entry)
 
@@ -403,7 +403,7 @@ def load_O_adsorption():
         "Rh": {(1, 0, 0): {}},
     }
 
-    with open(f"{TEST_DIR}/cs_entries_slabs.json") as file:
+    with open(f"{TEST_DIR}/cs_entries_slabs.json", encoding="utf-8") as file:
         entries = json.loads(file.read())
     for key in entries:
         entry = ComputedStructureEntry.from_dict(entries[key])
@@ -419,7 +419,7 @@ def load_O_adsorption():
                     clean = SlabEntry(entry.structure, entry.energy, (1, 0, 0), label=f"{key}_clean")
                     metals_O_entry_dict[el][1, 0, 0][clean] = []
 
-    with open(f"{TEST_DIR}/cs_entries_o_ads.json") as file:
+    with open(f"{TEST_DIR}/cs_entries_o_ads.json", encoding="utf-8") as file:
         entries = json.loads(file.read())
     for key in entries:
         entry = ComputedStructureEntry.from_dict(entries[key])

tests/analysis/test_transition_state.py

@@ -48,7 +48,7 @@ def test_run(self):
 
         neb_analysis1.setup_spline(spline_options={"saddle_point": "zero_slope"})
         assert_allclose(neb_analysis1.get_extrema()[1][0], (0.50023335723480078, 325.20003984140203))
-        with open(f"{TEST_DIR}/neb2/neb_analysis2.json") as file:
+        with open(f"{TEST_DIR}/neb2/neb_analysis2.json", encoding="utf-8") as file:
             neb_analysis2_dict = json.load(file)
         neb_analysis2 = NEBAnalysis.from_dict(neb_analysis2_dict)
         assert_allclose(neb_analysis2.get_extrema()[1][0], (0.37255257367467326, 562.40825334519991))

tests/analysis/test_wulff.py

@@ -23,7 +23,7 @@
 
 class TestWulffShape(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_DIR}/surface_samples.json") as data_file:
+        with open(f"{TEST_DIR}/surface_samples.json", encoding="utf-8") as data_file:
             surface_properties = json.load(data_file)
 
         surface_energies, miller_indices = {}, {}

tests/analysis/xas/test_spectrum.py

@@ -14,17 +14,17 @@
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/spectrum_test"
 
-with open(f"{TEST_DIR}/LiCoO2_k_xanes.json") as file:
+with open(f"{TEST_DIR}/LiCoO2_k_xanes.json", encoding="utf-8") as file:
     k_xanes_dict = json.load(file, cls=MontyDecoder)
-with open(f"{TEST_DIR}/LiCoO2_k_exafs.json") as file:
+with open(f"{TEST_DIR}/LiCoO2_k_exafs.json", encoding="utf-8") as file:
     k_exafs_dict = json.load(file, cls=MontyDecoder)
-with open(f"{TEST_DIR}/ZnO_l2_xanes.json") as file:
+with open(f"{TEST_DIR}/ZnO_l2_xanes.json", encoding="utf-8") as file:
     l2_xanes_dict = json.load(file, cls=MontyDecoder)
-with open(f"{TEST_DIR}/ZnO_l3_xanes.json") as file:
+with open(f"{TEST_DIR}/ZnO_l3_xanes.json", encoding="utf-8") as file:
     l3_xanes_dict = json.load(file, cls=MontyDecoder)
-with open(f"{TEST_DIR}/site1_k_xanes.json") as file:
+with open(f"{TEST_DIR}/site1_k_xanes.json", encoding="utf-8") as file:
     site1_xanes_dict = json.load(file, cls=MontyDecoder)
-with open(f"{TEST_DIR}/site2_k_xanes.json") as file:
+with open(f"{TEST_DIR}/site2_k_xanes.json", encoding="utf-8") as file:
     site2_xanes_dict = json.load(file, cls=MontyDecoder)