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)