Minor tests updates

doped/analysis.py

@@ -768,7 +768,7 @@ def __init__(
         if self.bulk_path is None:  # determine bulk_path to use
             if len(possible_bulk_folders) == 1:
                 self.bulk_path = os.path.join(self.output_path, possible_bulk_folders[0])
-            elif len([dir for dir in possible_bulk_folders if dir.endswith("_bulk")]) == 1:
+            elif len([dir for dir in possible_bulk_folders if str(dir).lower().endswith("_bulk")]) == 1:
                 self.bulk_path = os.path.join(
                     self.output_path,
                     next(iter(dir for dir in possible_bulk_folders if str(dir).lower().endswith("_bulk"))),

doped/thermodynamics.py

@@ -3768,12 +3768,12 @@ def _get_constrained_concentrations(
 
     def _get_in_gap_fermi_level_stability_window(self, defect_entry: Union[str, DefectEntry]) -> float:
         """
-        Convenience method to calculate the maximum difference between Fermi
-        levels at which ``defect_entry`` is the.
+        Convenience method to calculate the maximum difference between a Fermi
+        level at which ``defect_entry`` is the ground-state charge state, and
+        the band edges.
 
-        ground-state charge state, and the band edges (i.e. the
-        max of (CBM - lowest TL) and (highest TL - VBM) where
-        TL is any transition level involving ``defect_entry``).
+        i.e. taken from the minimum of (CBM - lowest TL) and (highest TL - VBM)
+        where TL is any transition level involving ``defect_entry``.
 
         Args:
             defect_entry (str or DefectEntry):
@@ -3946,7 +3946,7 @@ def _add_effective_dopant_concentration(
         {
             "Defect": "Dopant",
             "Charge": int(np.sign(effective_dopant_concentration)),
-            "Formation Energy (eV)": "N/A",
+            "Formation Energy (eV)": np.nan,
             "Concentration (cm^-3)": np.abs(effective_dopant_concentration),
             "Charge State Population": "100.0%",
         },
@@ -3957,7 +3957,11 @@ def _add_effective_dopant_concentration(
 
     for col in conc_df.columns:
         if col not in eff_dopant_df.columns:
-            eff_dopant_df[col] = "N/A"  # e.g. concentration per site, if per_site=True
+            # if string, set to "N/A":
+            if isinstance(conc_df[col].iloc[0], str):
+                eff_dopant_df[col] = "N/A"
+            else:
+                eff_dopant_df[col] = np.nan  # e.g. concentration per site, if per_site=True
 
     columns_to_drop = [col for col in eff_dopant_df.columns if col not in conc_df.columns]
     eff_dopant_df = eff_dopant_df.drop(columns=columns_to_drop)
@@ -3969,7 +3973,10 @@ def _group_defect_charge_state_concentrations(
     conc_df: pd.DataFrame, per_site: bool = False, skip_formatting: bool = False, lean: bool = False
 ):
     summed_df = conc_df.groupby("Defect").sum(numeric_only=True)  # auto-reordered by groupby sum
-    summed_df = summed_df.loc[conc_df["Defect"].unique()]  # retain ordering
+    defects = (
+        conc_df["Defect"] if "Defect" in conc_df.columns else conc_df.index.get_level_values("Defect")
+    )
+    summed_df = summed_df.loc[defects.unique()]  # retain ordering
     conc_column = next(k for k in conc_df.columns if k.startswith("Concentration"))
     raw_concentrations = (
         summed_df["Raw Concentration"]
@@ -4229,7 +4236,7 @@ def scissor_dos(delta_gap: float, dos: Union[Dos, FermiDos], tol: float = 1e-8,
     scissored_dos_dict["efermi"] -= np.float64(delta_gap / 2)
 
     if verbose:
-        print(f"Orig gap: {dos.get_gap(tol=tol)}, new gap:{dos.get_gap(tol=tol) + delta_gap}")
+        print(f"Orig gap: {dos.get_gap(tol=tol):.4f}, new gap:{dos.get_gap(tol=tol) + delta_gap:.4f}")
     scissored_dos_dict["structure"] = dos.structure.as_dict()
     if isinstance(dos, FermiDos):
         return FermiDos.from_dict(scissored_dos_dict)

tests/test_analysis.py

@@ -741,7 +741,7 @@ def test_extrinsic_Sb2Se3(self):
         # warning about negative corrections when using (fake) isotropic dielectric:
         Sb2Se3_O_dp, w = _create_dp_and_capture_warnings(
             output_path=f"{self.Sb2Se3_DATA_DIR}/defect",
-            bulk_path="bulk",
+            bulk_path=f"{self.Sb2Se3_DATA_DIR}/bulk",
             dielectric=40,  # fake isotropic dielectric
             parse_projected_eigen=False,
         )

tests/test_thermodynamics.py

@@ -216,7 +216,7 @@ def setUpClass(cls):
 
         cls.orig_MgO_defect_thermo = loadfn(os.path.join(cls.MgO_EXAMPLE_DIR, "MgO_thermo.json.gz"))
         cls.orig_MgO_defect_dict = loadfn(os.path.join(cls.MgO_EXAMPLE_DIR, "MgO_defect_dict.json.gz"))
-        cls.MgO_chempots = loadfn(os.path.join(cls.EXAMPLE_DIR, "CompetingPhases/MgO_chempots.json"))
+        cls.MgO_chempots = loadfn(os.path.join(cls.EXAMPLE_DIR, "MgO/CompetingPhases/MgO_chempots.json"))
 
         cls.Sb2O5_chempots = loadfn(os.path.join(data_dir, "Sb2O5/Sb2O5_chempots.json"))
         cls.orig_Sb2O5_defect_thermo = loadfn(os.path.join(data_dir, "Sb2O5/Sb2O5_thermo.json.gz"))
@@ -2706,13 +2706,13 @@ def test_prune_to_stable_entries(self):
             )
             == 2
         )
-        for i in ["sub_1_Te_on_Se_1", "sub_1_S_on_Se_1", "sub_1_O_on_Se_1", "inter_5_S_1", "inter_3_Te_1"]:
+        for i in ["sub_1_Te_on_Se_1", "sub_1_S_on_Se_1", "sub_1_O_on_Se_1", "inter_5_S_1"]:
             assert i in self.Se_ext_no_pnict_thermo.defect_entries, f"Checking {i}"
 
         pruned_Se_ext_no_pnict_thermo = self.Se_ext_no_pnict_thermo.prune_to_stable_entries()
         assert len(pruned_Se_ext_no_pnict_thermo) == 70
         assert len(pruned_Se_ext_no_pnict_thermo.transition_level_map) == 16
-        for i in ["sub_1_Te_on_Se_1", "sub_1_S_on_Se_1", "sub_1_O_on_Se_1", "inter_5_S_1", "inter_3_Te_1"]:
+        for i in ["sub_1_Te_on_Se_1", "sub_1_S_on_Se_1", "sub_1_O_on_Se_1", "inter_5_S_1"]:
             assert i not in pruned_Se_ext_no_pnict_thermo.defect_entries, f"Checking {i}"
         assert (
             len(
@@ -3085,9 +3085,9 @@ def test_get_fermi_level_and_concentrations(self):
             assert ("Orig gap:" in output) == kwargs.get("verbose", False)
             if kwargs.get("delta_gap") == 0.3 and kwargs.get("verbose", False):
                 if kwargs.get("tol") == 1e-1:
-                    assert "Orig gap: 2.7513, new gap:3.0513" in output
+                    assert "Orig gap: 2.7565, new gap:3.0565" in output
                 else:
-                    assert "Orig gap: 1.5126, new gap:1.8126" in output
+                    assert "Orig gap: 1.5178, new gap:1.8178" in output
                     assert np.isclose(fermi_level, 0.35124, atol=1e-3)  # different
 
             assert not w
@@ -3115,7 +3115,7 @@ def test_get_fermi_level_and_concentrations(self):
             )
             # Similar values to CdTe_LZ_Te_rich_concentrations.png, slightly different due to no scissoring
             assert (
-                np.isclose(fermi_level, 0.3396, atol=1e-3)
+                np.isclose(fermi_level, 0.3374, atol=1e-3)
                 == anneal_at_1000K_quench_at_RT_no_dopants_scissoring
             )
             assert (
@@ -3206,23 +3206,24 @@ def test_get_fermi_level_and_concentrations(self):
                     )
                     # Note that this check requires ``skip_formatting`` to be True as we don't format the
                     # dopant values here:
+                    expected_df = defect_thermo.get_equilibrium_concentrations(
+                        fermi_level=annealing_fermi_level,
+                        limit="Te-rich",
+                        temperature=kwargs.get("annealing_temperature", 1000),
+                        **{
+                            k: v
+                            for k, v in kwargs.items()
+                            if k not in ["return_annealing_values", "effective_dopant_concentration"]
+                        },
+                    )
                     expected_df = _add_effective_dopant_concentration(
-                        defect_thermo.get_equilibrium_concentrations(
-                            fermi_level=annealing_fermi_level,
-                            limit="Te-rich",
-                            temperature=kwargs.get("annealing_temperature", 1000),
-                            **{
-                                k: v
-                                for k, v in kwargs.items()
-                                if k not in ["return_annealing_values", "effective_dopant_concentration"]
-                            },
-                        ),
+                        expected_df,
                         kwargs.get("effective_dopant_concentration"),
                     )
                     if kwargs.get("per_charge", True):
                         conc_df_to_compare = conc_df.drop(columns=["Total Concentration (cm^-3)"])
-                    # replace NaNs with "N/A" (Dopant per site conc):
-                    conc_df_to_compare = conc_df_to_compare.fillna("N/A")
+                    else:
+                        conc_df_to_compare = conc_df
                     print(conc_df_to_compare, expected_df)  # for debugging
                     print(conc_df_to_compare.columns, expected_df.columns)  # for debugging
                     pd.testing.assert_frame_equal(conc_df_to_compare, expected_df)
@@ -3394,7 +3395,7 @@ def test_get_fermi_level_and_concentrations(self):
             "No chemical potentials supplied, so using 0 for all chemical potentials" in str(warn.message)
             for warn in w
         )
-        assert np.isclose(results[0], 1.1319, atol=1e-3)
+        assert np.isclose(results[0], 1.2737, atol=1e-3)
 
         defect_thermo = deepcopy(self.defect_thermo)
         defect_thermo.chempots = None
@@ -3413,7 +3414,7 @@ def test_get_in_gap_fermi_level_stability_window(self):
             ("v_Cd_0", 0.35),
             (self.defect_thermo.defect_entries["v_Cd_0"], 0.35),
             ("v_Cd_-2", 1.15),
-            ("Te_Cd_0", 1.374),  # this case, of being bounded by other charges on both sides,
+            ("Te_Cd_0", 1.162),  # this case, of being bounded by other charges on both sides,
             # wasn't tested with CdTe_example_thermo in DefectThermodynamicsTestCase
         ]:
             assert np.isclose(
@@ -3642,7 +3643,7 @@ def _array_from_conc_df(name):
         )
         ax.plot(
             self.anneal_temperatures,
-            _array_from_conc_df("Te_i_Td_Te2.83"),
+            _array_from_conc_df("Te_i_Td_Te2.83_a"),
             marker="o",
             label="$Te_i$",
             linestyle=":",