Don't let tests pollute the pymatgen repo

tests/alchemy/test_transmuters.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-import warnings
-
 from pymatgen.alchemy.filters import ContainsSpecieFilter
 from pymatgen.alchemy.transmuters import CifTransmuter, PoscarTransmuter
 from pymatgen.transformations.advanced_transformations import SuperTransformation
@@ -14,12 +12,6 @@
 
 
 class TestCifTransmuter(PymatgenTest):
-    def setUp(self):
-        warnings.simplefilter("ignore")
-
-    def tearDown(self):
-        warnings.simplefilter("default")
-
     def test_init(self):
         trans = []
         trans.append(SubstitutionTransformation({"Fe": "Mn", "Fe2+": "Mn2+"}))
@@ -77,9 +69,3 @@ def test_transmuter(self):
         assert tsc.transformed_structures[0].as_dict()["other_parameters"]["para1"] == "hello"
         tsc.add_tags(["world", "universe"])
         assert tsc.transformed_structures[0].as_dict()["other_parameters"]["tags"] == ["world", "universe"]
-
-
-if __name__ == "__main__":
-    import unittest
-
-    unittest.main()

tests/analysis/chemenv/connectivity/test_connected_components.py

@@ -2,7 +2,6 @@
 
 import copy
 import json
-import os
 
 import networkx as nx
 import numpy as np
@@ -847,12 +846,7 @@ def test_real_systems(self):
         assert ccs_periodicities == {"0D", "2D"}
 
     def test_coordination_sequences(self):
-        BaTiO3_se_fpath = os.path.join(
-            TEST_FILES_DIR,
-            "chemenv",
-            "structure_environments_files",
-            "se_mp-5020.json",
-        )
+        BaTiO3_se_fpath = f"{TEST_FILES_DIR}/chemenv/structure_environments/se_mp-5020.json"
         with open(BaTiO3_se_fpath) as file:
             dct = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dct)

tests/analysis/chemenv/connectivity/test_environment_nodes.py

@@ -1,9 +1,7 @@
 from __future__ import annotations
 
-import os
-
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
-from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pymatgen.util.testing import PymatgenTest
 
 try:
     import bson
@@ -12,12 +10,6 @@
 
 __author__ = "waroquiers"
 
-json_files_dir = os.path.join(
-    TEST_FILES_DIR,
-    "chemenv",
-    "json_test_files",
-)
-
 
 class TestEnvironmentNodes(PymatgenTest):
     def test_equal(self):
@@ -56,9 +48,3 @@ def test_str(self):
         struct = self.get_structure("SiO2")
         en = EnvironmentNode(central_site=struct[2], i_central_site=2, ce_symbol="T:4")
         assert str(en) == "Node #2 Si (T:4)"
-
-
-if __name__ == "__main__":
-    import unittest
-
-    unittest.main()

tests/analysis/chemenv/connectivity/test_structure_connectivity.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import json
-import os
 
 from pymatgen.analysis.chemenv.connectivity.connectivity_finder import ConnectivityFinder
 from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity
@@ -22,12 +21,7 @@
 
 class TestStructureConnectivity(PymatgenTest):
     def test_serialization(self):
-        BaTiO3_se_fpath = os.path.join(
-            TEST_FILES_DIR,
-            "chemenv",
-            "structure_environments_files",
-            "se_mp-5020.json",
-        )
+        BaTiO3_se_fpath = f"{TEST_FILES_DIR}/chemenv/structure_environments/se_mp-5020.json"
         with open(BaTiO3_se_fpath) as file:
             dd = json.load(file)
         struct_envs = StructureEnvironments.from_dict(dd)

tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-import os
-
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
@@ -18,11 +16,7 @@
 
 __author__ = "waroquiers"
 
-json_files_dir = os.path.join(
-    TEST_FILES_DIR,
-    "chemenv",
-    "json_test_files",
-)
+json_dir = f"{TEST_FILES_DIR}/chemenv/json"
 
 
 class TestCoordinationGeometryFinder(PymatgenTest):
@@ -125,13 +119,13 @@ def test_abstract_geometry(self):
 
     # def _strategy_test(self, strategy):
     #     files = []
-    #     for _dirpath, _dirnames, filenames in os.walk(json_files_dir):
+    #     for _dirpath, _dirnames, filenames in os.walk(json_dir):
     #         files.extend(filenames)
     #         break
 
     #     for _ifile, json_file in enumerate(files):
     #         with self.subTest(json_file=json_file):
-    #             with open(f"{json_files_dir}/{json_file}") as f:
+    #             with open(f"{json_dir}/{json_file}") as f:
     #                 dd = json.load(f)
 
     #             atom_indices = dd["atom_indices"]

tests/analysis/chemenv/coordination_environments/test_read_write.py

@@ -2,7 +2,6 @@
 
 import json
 import os
-import shutil
 import unittest
 
 from numpy.testing import assert_allclose, assert_array_almost_equal
@@ -29,8 +28,8 @@
 
 __author__ = "waroquiers"
 
-json_files_dir = f"{TEST_FILES_DIR}/chemenv/json_test_files"
-se_files_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments_files"
+json_dir = f"{TEST_FILES_DIR}/chemenv/json"
+struct_env_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments"
 
 
 class TestReadWriteChemenv(unittest.TestCase):
@@ -41,7 +40,7 @@ def setUpClass(cls):
         os.makedirs("tmp_dir", exist_ok=True)
 
     def test_read_write_structure_environments(self):
-        with open(f"{json_files_dir}/test_T--4_FePO4_icsd_4266.json") as file:
+        with open(f"{json_dir}/test_T--4_FePO4_icsd_4266.json") as file:
             dd = json.load(file)
 
         atom_indices = dd["atom_indices"]
@@ -76,7 +75,7 @@ def test_read_write_structure_environments(self):
         # assert lse == lse2
 
     def test_structure_environments_neighbors_sets(self):
-        with open(f"{se_files_dir}/se_mp-7000.json") as f:
+        with open(f"{struct_env_dir}/se_mp-7000.json") as f:
             dd = json.load(f)
 
         struct_envs = StructureEnvironments.from_dict(dd)
@@ -221,26 +220,21 @@ def test_strategies(self):
         assert multi_weights_strategy_2 != multi_weights_strategy_3
 
     def test_read_write_voronoi(self):
-        with open(f"{json_files_dir}/test_T--4_FePO4_icsd_4266.json") as f:
-            dd = json.load(f)
+        with open(f"{json_dir}/test_T--4_FePO4_icsd_4266.json") as file:
+            dd = json.load(file)
 
         struct = Structure.from_dict(dd["structure"])
 
         valences = [site.specie.oxi_state for site in struct]
 
         detailed_voronoi_container = DetailedVoronoiContainer(structure=struct, valences=valences)
 
-        with open("tmp_dir/se.json", "w") as f:
-            json.dump(detailed_voronoi_container.as_dict(), f)
+        with open("tmp_dir/se.json", "w") as file:
+            json.dump(detailed_voronoi_container.as_dict(), file)
 
-        with open("tmp_dir/se.json") as f:
-            dd = json.load(f)
+        with open("tmp_dir/se.json") as file:
+            dd = json.load(file)
 
         detailed_voronoi_container2 = DetailedVoronoiContainer.from_dict(dd)
 
         assert detailed_voronoi_container == detailed_voronoi_container2
-
-    @classmethod
-    def tearDownClass(cls):
-        # Remove the directory in which the temporary files have been created
-        shutil.rmtree("tmp_dir")

tests/analysis/chemenv/coordination_environments/test_structure_environments.py

@@ -22,12 +22,12 @@
 
 __author__ = "waroquiers"
 
-struct_env_files_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments_files"
+struct_env_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments"
 
 
 class TestStructureEnvironments(PymatgenTest):
     def test_structure_environments(self):
-        with open(f"{struct_env_files_dir}/se_mp-7000.json") as f:
+        with open(f"{struct_env_dir}/se_mp-7000.json") as f:
             dd = json.load(f)
 
         struct_envs = StructureEnvironments.from_dict(dd)
@@ -118,7 +118,7 @@ def test_structure_environments(self):
         assert ce != ce2
 
     def test_light_structure_environments(self):
-        with open(f"{struct_env_files_dir}/se_mp-7000.json") as f:
+        with open(f"{struct_env_dir}/se_mp-7000.json") as f:
             dd = json.load(f)
 
         struct_envs = StructureEnvironments.from_dict(dd)

tests/analysis/chemenv/coordination_environments/test_voronoi.py

@@ -11,7 +11,6 @@
 
 __author__ = "waroquiers"
 
-json_files_dir = f"{TEST_FILES_DIR}/chemenv/json_test_files"
 img_files_dir = f"{TEST_FILES_DIR}/chemenv/images"
 
 

tests/analysis/chemenv/coordination_environments/test_weights.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import json
-import os
 
 import pytest
 from pytest import approx
@@ -21,11 +20,7 @@
 
 __author__ = "waroquiers"
 
-se_files_dir = os.path.join(
-    TEST_FILES_DIR,
-    "chemenv",
-    "structure_environments_files",
-)
+struct_env_dir = f"{TEST_FILES_DIR}/chemenv/structure_environments"
 
 
 class FakeNbSet:
@@ -248,7 +243,7 @@ def test_CN_bias_weight(self):
 
     def test_self_csms_weight(self):
         # Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
-        with open(f"{se_files_dir}/se_mp-743972.json") as f:
+        with open(f"{struct_env_dir}/se_mp-743972.json") as f:
             dct = json.load(f)
         struct_envs = StructureEnvironments.from_dict(dct)
 
@@ -324,7 +319,7 @@ def test_self_csms_weight(self):
         assert abs(self_w - 0.14204073172729198) < 1e-8
 
         # Get the StructureEnvironments for SiO2 (mp-7000)
-        with open(f"{se_files_dir}/se_mp-7000.json") as f:
+        with open(f"{struct_env_dir}/se_mp-7000.json") as f:
             dct = json.load(f)
         struct_envs = StructureEnvironments.from_dict(dct)
 
@@ -368,7 +363,7 @@ def test_self_csms_weight(self):
 
     def test_delta_csms_weight(self):
         # Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
-        with open(f"{se_files_dir}/se_mp-743972.json") as f:
+        with open(f"{struct_env_dir}/se_mp-743972.json") as f:
             dd = json.load(f)
         struct_envs = StructureEnvironments.from_dict(dd)
 
@@ -500,7 +495,7 @@ def test_delta_csms_weight(self):
         assert abs(delta_w - 0.103515625) < 1e-8
 
         # Get the StructureEnvironments for SiO2 (mp-7000)
-        with open(f"{se_files_dir}/se_mp-7000.json") as f:
+        with open(f"{struct_env_dir}/se_mp-7000.json") as f:
             dd = json.load(f)
         struct_envs = StructureEnvironments.from_dict(dd)
 

tests/analysis/chemenv/utils/test_graph_utils.py

@@ -695,9 +695,3 @@ def test_cycle(self):
         assert c1 == c2
         c2 = MultiGraphCycle([e2, e3, e1], [1, 2, 0])
         assert c1 == c2
-
-
-if __name__ == "__main__":
-    import unittest
-
-    unittest.main()

tests/analysis/elasticity/test_elastic.py

@@ -265,10 +265,6 @@ def setUp(self):
         self.exp_cu = ElasticTensorExpansion([cu_c2, cu_c3])
         cu_c4 = Tensor.from_voigt(self.data_dict["Cu_fourth_order"])
         self.exp_cu_4 = ElasticTensorExpansion([cu_c2, cu_c3, cu_c4])
-        warnings.simplefilter("ignore")
-
-    def tearDown(self):
-        warnings.simplefilter("default")
 
     def test_init(self):
         c_ijkl = Tensor.from_voigt(self.c2)

tests/analysis/gb/test_grain.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-import warnings
-
 import numpy as np
 from numpy.testing import assert_allclose
 from pytest import approx
@@ -21,7 +19,6 @@
 class TestGrainBoundary(PymatgenTest):
     @classmethod
     def setUpClass(cls):
-        warnings.filterwarnings("ignore")
         cls.Cu_conv = Structure.from_file(f"{test_dir}/Cu_mp-30_conventional_standard.cif")
         GB_Cu_conv = GrainBoundaryGenerator(cls.Cu_conv)
         cls.Cu_GB1 = GB_Cu_conv.gb_from_parameters(
@@ -42,10 +39,6 @@ def setUpClass(cls):
             rm_ratio=0.0,
         )
 
-    @classmethod
-    def tearDownClass(cls):
-        warnings.simplefilter("default")
-
     def test_init(self):
         assert self.Cu_GB1.rotation_angle == approx(123.74898859588858)
         assert self.Cu_GB1.vacuum_thickness == approx(1.5)
@@ -114,7 +107,6 @@ def test_as_dict_and_from_dict(self):
 class TestGrainBoundaryGenerator(PymatgenTest):
     @classmethod
     def setUpClass(cls):
-        warnings.filterwarnings("ignore")
         cls.Cu_prim = Structure.from_file(f"{test_dir}/Cu_mp-30_primitive.cif")
         cls.GB_Cu_prim = GrainBoundaryGenerator(cls.Cu_prim)
         cls.Cu_conv = Structure.from_file(f"{test_dir}/Cu_mp-30_conventional_standard.cif")
@@ -128,10 +120,6 @@ def setUpClass(cls):
         cls.Bi = Structure.from_file(f"{test_dir}/Bi_mp-23152_primitive.cif")
         cls.GB_Bi = GrainBoundaryGenerator(cls.Bi)
 
-    @classmethod
-    def tearDownClass(cls):
-        warnings.simplefilter("default")
-
     def test_gb_from_parameters(self):
         # from fcc primitive cell,axis[1,2,3],sigma 9.
         gb_cu_123_prim1 = self.GB_Cu_prim.gb_from_parameters([1, 2, 3], 123.74898859588858, expand_times=2)

tests/analysis/magnetism/test_analyzer.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import unittest
-import warnings
 from shutil import which
 
 import pytest
@@ -66,11 +65,6 @@ def setUp(self):
         coords = [[0.5, 0.5, 0.5], [0, 0, 0], [0, 0.5, 0], [0.5, 0, 0.5]]
         self.NiO_unphysical = Structure(latt, species, coords, site_properties={"magmom": [-3, 0, 0, 0]})
 
-        warnings.simplefilter("ignore")
-
-    def tearDown(self):
-        warnings.simplefilter("default")
-
     def test_get_representations(self):
         # tests to convert between storing magnetic moment information
         # on site_properties or on Species 'spin' property