Tests: Avoid vise suppression of warnings

doped/core.py

@@ -251,10 +251,15 @@ def from_dict(cls, d: dict):
         Returns:
             ``DefectEntry`` object
         """
-        from doped.utils.parsing import suppress_logging
+        from doped.utils.parsing import _reset_warnings, suppress_logging
 
         with suppress_logging():
-            return super().from_dict(d)
+            obj = super().from_dict(d)
+
+        _reset_warnings()  # vise suppresses ``UserWarning``s (and this initialises ``vise``
+        # ``BandEdgeStates`` objects) so need to reset
+
+        return obj
 
     def _check_correction_error_and_return_output(
         self,
@@ -598,10 +603,13 @@ def _load_and_parse_eigenvalue_data(
         from doped.utils.parsing import (
             _get_output_files_and_check_if_multiple,
             _multiple_files_warning,
+            _reset_warnings,
             get_procar,
             get_vasprun,
         )
 
+        _reset_warnings()  # vise suppresses `UserWarning`s, so need to reset
+
         parsed_vr_procar_dict = {}
         for vr, procar, label in [(bulk_vr, bulk_procar, "bulk"), (defect_vr, defect_procar, "defect")]:
             path = self.calculation_metadata.get(f"{label}_path")
@@ -782,6 +790,9 @@ def get_eigenvalue_analysis(
             ``Figure`` object (if ``plot=True``).
         """
         from doped.utils.eigenvalues import get_eigenvalue_analysis
+        from doped.utils.parsing import _reset_warnings
+
+        _reset_warnings()  # vise suppresses `UserWarning`s, so need to reset
 
         self._load_and_parse_eigenvalue_data(
             bulk_vr=bulk_vr,

doped/corrections.py

@@ -36,7 +36,6 @@
 """
 
 import os
-import warnings
 from typing import Optional, Union
 
 import matplotlib.pyplot as plt
@@ -49,21 +48,18 @@
 from pymatgen.io.vasp.outputs import Locpot, Outcar
 from shakenbreak.plotting import _install_custom_font
 
-from doped import _ignore_pmg_warnings
 from doped.analysis import _convert_dielectric_to_tensor
 from doped.utils.parsing import (
     _get_bulk_supercell,
     _get_defect_supercell,
     _get_defect_supercell_bulk_site_coords,
+    _reset_warnings,
     get_locpot,
     get_outcar,
 )
 from doped.utils.plotting import _get_backend, format_defect_name
 
-warnings.simplefilter("default")
-# `message` only needs to match start of message:
-warnings.filterwarnings("ignore", message="`np.int` is a deprecated alias for the builtin `int`")
-warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
+_reset_warnings()  # vise suppresses `UserWarning`s, so need to reset
 
 
 def _monty_decode_nested_dicts(d):
@@ -418,11 +414,7 @@ def get_kumagai_correction(
             "You can do this by running `pip install pydefect`."
         ) from exc
 
-    # vise suppresses `UserWarning`s, so need to reset
-    warnings.simplefilter("default")
-    warnings.filterwarnings("ignore", message="`np.int` is a deprecated alias for the builtin `int`")
-    warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
-    _ignore_pmg_warnings()
+    _reset_warnings()  # vise suppresses `UserWarning`s, so need to reset
 
     def doped_make_efnv_correction(
         charge: float,

doped/utils/eigenvalues.py

@@ -22,9 +22,13 @@
 from pymatgen.io.vasp.outputs import Procar, Vasprun
 from shakenbreak.plotting import _install_custom_font
 
-from doped import _ignore_pmg_warnings
 from doped.core import DefectEntry
-from doped.utils.parsing import get_magnetization_from_vasprun, get_nelect_from_vasprun, get_procar
+from doped.utils.parsing import (
+    _reset_warnings,
+    get_magnetization_from_vasprun,
+    get_nelect_from_vasprun,
+    get_procar,
+)
 from doped.utils.plotting import _get_backend
 
 if TYPE_CHECKING:
@@ -52,11 +56,7 @@
         "You can do this by running `pip install pydefect`."
     ) from exc
 
-# vise suppresses `UserWarning`s, so need to reset
-warnings.simplefilter("default")
-warnings.filterwarnings("ignore", message="`np.int` is a deprecated alias for the builtin `int`")
-warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
-_ignore_pmg_warnings()
+_reset_warnings()  # vise suppresses `UserWarning`s, so need to reset
 
 
 def _coordination(self, include_on_site=True, cutoff_factor=None) -> "Coordination":

doped/utils/parsing.py

@@ -33,6 +33,17 @@ def _get_potcar_summary_stats() -> dict:
     return loadfn(POTCAR_STATS_PATH)
 
 
+def _reset_warnings():
+    """
+    When importing ``vise``/``pydefect``, ``UserWarning``s are suppressed, so
+    we need to reset.
+    """
+    warnings.simplefilter("default")
+    warnings.filterwarnings("ignore", message="`np.int` is a deprecated alias for the builtin `int`")
+    warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
+    _ignore_pmg_warnings()
+
+
 @contextlib.contextmanager
 def suppress_logging(level=logging.CRITICAL):
     """
@@ -542,11 +553,7 @@ def check_atom_mapping_far_from_defect(bulk, defect, defect_coords):
     except ImportError:  # can't check as vise/pydefect not installed. Not critical so just return
         return
 
-    # vise suppresses `UserWarning`s, so need to reset
-    warnings.simplefilter("default")
-    warnings.filterwarnings("ignore", message="`np.int` is a deprecated alias for the builtin `int`")
-    warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
-    _ignore_pmg_warnings()
+    _reset_warnings()  # vise suppresses `UserWarning`s, so need to reset
 
     far_from_defect_disps = {site.specie.symbol: [] for site in bulk}
 

tests/test_thermodynamics.py

@@ -99,7 +99,7 @@ def setUp(self):
         self.MgO_defect_thermo = deepcopy(self.orig_MgO_defect_thermo)
         self.MgO_defect_dict = deepcopy(self.orig_MgO_defect_dict)
         self.Sb2O5_defect_thermo = deepcopy(self.orig_Sb2O5_defect_thermo)
-        self.Zns_defect_thermo = deepcopy(self.orig_ZnS_defect_thermo)
+        self.ZnS_defect_thermo = deepcopy(self.orig_ZnS_defect_thermo)
 
     @classmethod
     def setUpClass(cls):
@@ -175,8 +175,8 @@ def _compare_defect_thermo_and_dict(self, defect_thermo, defect_dict):
             round(entry.get_ediff(), 3) for entry in defect_dict.values()
         }
         assert {  # check coords are the same by getting their products
-            round(np.product(entry.sc_defect_frac_coords), 3) for entry in defect_thermo.defect_entries
-        } == {round(np.product(entry.sc_defect_frac_coords), 3) for entry in defect_dict.values()}
+            round(np.prod(entry.sc_defect_frac_coords), 3) for entry in defect_thermo.defect_entries
+        } == {round(np.prod(entry.sc_defect_frac_coords), 3) for entry in defect_dict.values()}
 
     def _compare_defect_thermos(self, defect_thermo1, defect_thermo2):
         assert len(defect_thermo1.defect_entries) == len(defect_thermo2.defect_entries)
@@ -187,8 +187,8 @@ def _compare_defect_thermos(self, defect_thermo1, defect_thermo2):
             round(entry.get_ediff(), 3) for entry in defect_thermo2.defect_entries
         }
         assert {  # check coords are the same by getting their products
-            round(np.product(entry.sc_defect_frac_coords), 3) for entry in defect_thermo1.defect_entries
-        } == {round(np.product(entry.sc_defect_frac_coords), 3) for entry in defect_thermo2.defect_entries}
+            round(np.prod(entry.sc_defect_frac_coords), 3) for entry in defect_thermo1.defect_entries
+        } == {round(np.prod(entry.sc_defect_frac_coords), 3) for entry in defect_thermo2.defect_entries}
 
     def _check_defect_thermo(
         self,
@@ -228,8 +228,8 @@ def _check_defect_thermo(
         defect_thermo.to_json()  # test default naming
         compositions = ["CdTe", "Y2Ti2S2O5", "Sb2Se3", "SiSbTe3", "V2O5", "MgO", "Sb2O5", "ZnS"]
         assert defect_thermo.bulk_formula in compositions
+        assert any(os.path.exists(f"{i}_defect_thermodynamics.json") for i in compositions)
         for i in compositions:
-            os.path.exists(f"{i}_defect_thermodynamics.json")
             if_present_rm(f"{i}_defect_thermodynamics.json")
 
         thermo_dict = defect_thermo.as_dict()
@@ -446,7 +446,7 @@ def test_DefectsParser_thermo_objs(self):
             (self.V2O5_defect_thermo, "V2O5_defect_thermo"),
             (self.MgO_defect_thermo, "MgO_defect_thermo"),
             (self.Sb2O5_defect_thermo, "Sb2O5_defect_thermo"),
-            (self.Zns_defect_thermo, "ZnS_defect_thermo"),
+            (self.ZnS_defect_thermo, "ZnS_defect_thermo"),
         ]:
             print(f"Checking {name}")
             if "V2O5" in name:
@@ -475,7 +475,7 @@ def test_DefectsParser_thermo_objs(self):
     def test_DefectsParser_thermo_objs_no_metadata(self):
         """
         Test the `DefectThermodynamics` objects created from the
-        `DefectsParser.get_defect_thermodynamics()` method.
+        ``DefectsParser.get_defect_thermodynamics()`` method.
         """
         for defect_thermo, name in [
             (self.CdTe_defect_thermo, "CdTe_defect_thermo"),
@@ -485,11 +485,16 @@ def test_DefectsParser_thermo_objs_no_metadata(self):
             (self.V2O5_defect_thermo, "V2O5_defect_thermo"),
             (self.MgO_defect_thermo, "MgO_defect_thermo"),
             (self.Sb2O5_defect_thermo, "Sb2O5_defect_thermo"),
-            (self.Zns_defect_thermo, "ZnS_defect_thermo"),
+            (self.ZnS_defect_thermo, "ZnS_defect_thermo"),
         ]:
             print(f"Checking {name}")
-            defect_entries_wout_metadata = defect_thermo.defect_entries
+            # get set of random 7 entries from defect_entries_wout_metadata (7 because need full CdTe
+            # example set for its semi-hard 😏 tests)
+            defect_entries_wout_metadata = random.sample(
+                defect_thermo.defect_entries, min(7, len(defect_thermo.defect_entries))
+            )
             for entry in defect_entries_wout_metadata:
+                print(f"Setting metadata to empty for {entry.name}")
                 entry.calculation_metadata = {}
 
             with pytest.raises(ValueError) as exc:
@@ -512,8 +517,11 @@ def test_DefectsParser_thermo_objs_no_metadata(self):
             )
             self._check_defect_thermo(thermo_wout_metadata)  # default values
 
-            defect_entries_wout_metadata_or_degeneracy = defect_thermo.defect_entries
+            defect_entries_wout_metadata_or_degeneracy = random.sample(
+                defect_thermo.defect_entries, min(7, len(defect_thermo.defect_entries))
+            )  # get set of random 7 entries from defect_entries_wout_metadata (7 needed for CdTe tests)
             for entry in defect_entries_wout_metadata_or_degeneracy:
+                print(f"Setting metadata and degeneracy factors to empty for {entry.name}")
                 entry.calculation_metadata = {}
                 entry.degeneracy_factors = {}
 
@@ -524,7 +532,7 @@ def test_DefectsParser_thermo_objs_no_metadata(self):
             symm_df = thermo_wout_metadata_or_degeneracy.get_symmetries_and_degeneracies()
             assert symm_df["g_Spin"].apply(lambda x: isinstance(x, int)).all()
 
-            for defect_entry in defect_thermo.defect_entries:
+            for defect_entry in defect_entries_wout_metadata_or_degeneracy:
                 assert defect_entry.degeneracy_factors["spin degeneracy"] in {1, 2}
                 assert isinstance(
                     defect_entry.degeneracy_factors["orientational degeneracy"], (int, float)