Use issubclass rather than isinstance

SMTG-Bham · Jul 12, 2024 · 2ef401e · 2ef401e
1 parent a0a8139
commit 2ef401e
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Showing 2 changed files with 16 additions and 14 deletions.
diff --git a/shakenbreak/energy_lowering_distortions.py b/shakenbreak/energy_lowering_distortions.py
@@ -273,6 +273,13 @@ def _prune_dict_across_charges(
                 defect_species_snb_name = f"{defect}_{'+' if charge > 0 else ''}{charge}"
                 for i in ["+", "", "+"]:  # back to SnB name with "+" if all fail
                     defect_species = defect_species_snb_name.replace("+", i)  # try with and without '+'
+                    distorted_struct = distortion_dict["structures"][0]
+                    if not isinstance(distorted_struct, Structure):
+                        raise ValueError(
+                            f"Distorted structure for {defect_species} was not correctly parsed. Instead "
+                            f"of a pymatgen Structure object, got: {type(distorted_struct)}; "
+                            f"{distorted_struct}"
+                        )
                     comparison_results = compare_struct_to_distortions(
                         distortion_dict["structures"][0],
                         defect_species,
@@ -460,7 +467,7 @@ def get_energy_lowering_distortions(
                         structure_filename=structure_filename,
                     )  # get the final structure of the
                     # energy lowering distortion
-                    if any(isinstance(warning.category, UserWarning) for warning in w):
+                    if any(issubclass(warning.category, UserWarning) for warning in w):
                         # problem parsing structure, user will have received appropriate
                         # warning from io.read_vasp_structure()
                         print(
@@ -532,7 +539,7 @@ def get_energy_lowering_distortions(
                             structure_path=f"{output_path}/{defect_species}/{bond_distortion}",
                             structure_filename=structure_filename,
                         )
-                        if any(isinstance(warning.category, UserWarning) for warning in w):
+                        if any(issubclass(warning.category, UserWarning) for warning in w):
                             # problem parsing structure, user will have received appropriate
                             # warning from io.read_vasp_structure()
                             print(

diff --git a/tests/test_energy_lowering_distortions.py b/tests/test_energy_lowering_distortions.py
@@ -45,13 +45,13 @@ def setUp(self):
         self.FHI_AIMS_DATA_DIR = os.path.join(self.DATA_DIR, "fhi_aims")
         self.ESPRESSO_DATA_DIR = os.path.join(self.DATA_DIR, "quantum_espresso")
         self.V_Cd_minus_0pt55_structure = Structure.from_file(
-            self.VASP_CDTE_DATA_DIR + "/vac_1_Cd_0/Bond_Distortion_-55.0%/CONTCAR"
+            f"{self.VASP_CDTE_DATA_DIR}/vac_1_Cd_0/Bond_Distortion_-55.0%/CONTCAR"
         )
 
         # create fake distortion folders for testing functionality:
         for defect_dir in ["Int_Cd_2_+1", "vac_1_Cd_-1", "vac_1_Cd_-2"]:
             if not os.path.exists(f"{self.VASP_CDTE_DATA_DIR}/{defect_dir}"):
-                os.mkdir(self.VASP_CDTE_DATA_DIR + f"/{defect_dir}")
+                os.mkdir(f"{self.VASP_CDTE_DATA_DIR}/{defect_dir}")
         # Int_Cd_2_+1 without data, to test warnings
         V_Cd_1_dict = {"distortions": {-0.075: -205.740}, "Unperturbed": -205.800}
         dumpfn(
@@ -79,16 +79,10 @@ def setUp(self):
             "sub_1_In_on_Cd_+1",
         ]
 
-        self.orig_castep_0pt3_files = os.listdir(
-            self.CASTEP_DATA_DIR + "/vac_1_Cd_0/Bond_Distortion_30.0%"
-        )
-        self.orig_cp2k_0pt3_files = os.listdir(self.CP2K_DATA_DIR + "/vac_1_Cd_0/Bond_Distortion_30.0%")
-        self.orig_fhi_aims_0pt3_files = os.listdir(
-            self.FHI_AIMS_DATA_DIR + "/vac_1_Cd_0/Bond_Distortion_30.0%"
-        )
-        self.orig_espresso_0pt3_files = os.listdir(
-            self.ESPRESSO_DATA_DIR + "/vac_1_Cd_0/Bond_Distortion_30.0%"
-        )
+        self.orig_castep_0pt3_files = os.listdir(f"{self.CASTEP_DATA_DIR}/vac_1_Cd_0/Bond_Distortion_30.0%")
+        self.orig_cp2k_0pt3_files = os.listdir(f"{self.CP2K_DATA_DIR}/vac_1_Cd_0/Bond_Distortion_30.0%")
+        self.orig_fhi_aims_0pt3_files = os.listdir(f"{self.FHI_AIMS_DATA_DIR}/vac_1_Cd_0/Bond_Distortion_30.0%")
+        self.orig_espresso_0pt3_files = os.listdir(f"{self.ESPRESSO_DATA_DIR}/vac_1_Cd_0/Bond_Distortion_30.0%")
 
     def tearDown(self):
         # removed generated folders
@@ -228,6 +222,7 @@ def test_get_energy_lowering_distortions(self):
             low_energy_defects_dict = energy_lowering_distortions.get_energy_lowering_distortions(
                 self.defect_charges_dict, self.VASP_CDTE_DATA_DIR
             )
+        print([str(warning.message) for warning in w])  # for debugging
         mock_print.assert_any_call("\nvac_1_Cd")
         mock_print.assert_any_call(
             "vac_1_Cd_0: Energy difference between minimum, found with -0.55 bond distortion, "