Update tests

doped/core.py

@@ -1223,9 +1223,15 @@ def __repr__(self):
  def __eq__(self, other):
  """
  Determine whether two ``DefectEntry`` objects are equal, by comparing
- self.name and self.sc_entry.
+ ``self.name``, ``self.sc_entry``, ``self.bulk_entry`` and
+ ``self.corrections`` (i.e. name and energy match).
  """
- return self.name == other.name and self.sc_entry == other.sc_entry
+ return (
+ self.name == other.name
+ and self.sc_entry == other.sc_entry
+ and self.bulk_entry == other.bulk_entry
+ and self.corrections == other.corrections
+ )
 
  @property
  def bulk_entry_energy(self):

doped/thermodynamics.py

@@ -1303,8 +1303,9 @@ def get_equilibrium_concentrations(
  conc_df = pd.DataFrame(energy_concentration_list)
 
  if per_charge:
- if skip_formatting:
+ if lean:
  return conc_df
+
  conc_df["Charge State Population"] = conc_df["Raw Concentration"] / conc_df.groupby("Defect")[
  "Raw Concentration"
  ].transform("sum")
@@ -1688,15 +1689,16 @@ def get_quenched_fermi_level_and_concentrations(
  )
 
  def _get_constrained_concentrations(
- fermi_level, per_charge=True, per_site=False, skip_formatting=False
+ fermi_level, per_charge=True, per_site=False, skip_formatting=False, lean=True
  ):
  conc_df = self.get_equilibrium_concentrations(
  chempots=chempots,
  limit=limit,
  el_refs=el_refs,
  temperature=quenched_temperature,
  fermi_level=fermi_level,
- lean=True,
+ skip_formatting=True,
+ lean=lean,
  )
  conc_df["Total Concentration (cm^-3)"] = conc_df["Defect"].map(total_concentrations)
  conc_df["Concentration (cm^-3)"] = ( # set total concentration to match annealing conc
@@ -1768,7 +1770,9 @@ def _get_constrained_total_q(fermi_level):
  eq_fermi_level,
  e_conc,
  h_conc,
- _get_constrained_concentrations(eq_fermi_level, per_charge, per_site, skip_formatting),
+ _get_constrained_concentrations(
+ eq_fermi_level, per_charge, per_site, skip_formatting, lean=False
+ ), # not lean for final output
  )
 
  def get_formation_energy(

tests/test_generation.py

@@ -6,7 +6,6 @@
 
 import copy
 import filecmp
-import json
 import operator
 import os
 import random
@@ -21,7 +20,6 @@
 import numpy as np
 import pytest
 from ase.build import bulk, make_supercell
-from monty.json import MontyEncoder
 from monty.serialization import dumpfn, loadfn
 from pymatgen.analysis.defects.core import DefectType
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
@@ -62,6 +60,28 @@ def _potcars_available() -> bool:
  return False
 
 
+def _compare_attributes(obj1, obj2, exclude=None):
+ """
+ Check that two objects are equal by comparing their public
+ attributes/properties.
+ """
+ if exclude is None:
+ exclude = set() # Create an empty set if no exclusions
+
+ for attr in dir(obj1):
+ if attr.startswith("_") or attr in exclude or callable(getattr(obj1, attr)):
+ continue # Skip private, excluded, and callable attributes
+
+ print(attr)
+ val1 = getattr(obj1, attr)
+ val2 = getattr(obj2, attr)
+
+ if isinstance(val1, np.ndarray):
+ assert np.allclose(val1, val2)
+ else:
+ assert val1 == val2
+
+
 class DefectsGeneratorTest(unittest.TestCase):
  def setUp(self):
  # don't run heavy tests on GH Actions, these are run locally (too slow without multiprocessing etc)
@@ -667,7 +687,7 @@ def _save_defect_gen_jsons(self, defect_gen):
  if_present_rm("test.json")
  if_present_rm("test_defect_gen.json")
 
- def _load_and_test_defect_gen_jsons(self, defect_gen): # , gen_check): - shouldn't need this as we
+ def _load_and_test_defect_gen_jsons(self, defect_gen):
  # test that the jsons are identical (except for ordering)
  formula, _fu = defect_gen.primitive_structure.composition.get_reduced_formula_and_factor(
  iupac_ordering=True
@@ -683,9 +703,7 @@ def _load_and_test_defect_gen_jsons(self, defect_gen): # , gen_check): - should
 
  # test it's the same as the original:
  # here we compare using json dumps because the ordering can change slightly when saving to json
- assert json.dumps(defect_gen_from_json, sort_keys=True, cls=MontyEncoder) == json.dumps(
- defect_gen, sort_keys=True, cls=MontyEncoder
- )
+ _compare_attributes(defect_gen, defect_gen_from_json)
  if_present_rm("test.json")
  if_present_rm("test_loadfn.json")
  if_present_rm(default_json_filename)
@@ -2016,7 +2034,7 @@ def test_defects_generator_CdTe(self):
  for warning in w
  if ("`calculation_metadata` attribute is not set") not in str(warning.message)
  ]
- assert len(non_ignored_warnings) == 0 # no warnings for CdTe, scalar matrix
+ assert not non_ignored_warnings # no warnings for CdTe, scalar matrix
 
  def test_defects_generator_CdTe_supercell_input(self):
  CdTe_defect_gen, output = self._generate_and_test_no_warnings(self.CdTe_bulk_supercell)
@@ -3246,10 +3264,10 @@ def test_agsbte2(self):
  self.sqs_agsbte2, generate_supercell=False
  )
  # same output regardless of `generate_supercell` because input supercell satisfies constraints
+ with pytest.raises(AssertionError):
+ _compare_attributes(agsbte2_defect_gen_a, agsbte2_defect_gen_b)
  agsbte2_defect_gen_a.generate_supercell = False # adjust one difference to make equal overall
- assert json.dumps(agsbte2_defect_gen_a, sort_keys=True, cls=MontyEncoder) == json.dumps(
- agsbte2_defect_gen_b, sort_keys=True, cls=MontyEncoder
- )
+ _compare_attributes(agsbte2_defect_gen_a, agsbte2_defect_gen_b)
  assert np.allclose(
  agsbte2_defect_gen_a.supercell_matrix,
  np.array([[3.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]),