Avoid new spglib deprecation warning

doped/__init__.py

@@ -64,17 +64,16 @@ def _ignore_pmg_warnings():
     warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
     warnings.filterwarnings("ignore", message="Use of properties is now deprecated")
 
-    warnings.filterwarnings("ignore", message="get_vasp_input")  # deprecation warning introduced
-    # in pymatgen>2024.1.6, fixed in our PR: https://github.com/materialsproject/pymatgen/pull/3601
-    # (now merged) -- delete later if pymatgen requirement is updated beyond this
-
     # avoid warning about selective_dynamics properties (can happen if user explicitly set "T T T" (or
     # otherwise) for the bulk):
     warnings.filterwarnings("ignore", message="Not all sites have property")
 
     # ignore warning about structure charge that appears when getting Vasprun.as_dict():
     warnings.filterwarnings("ignore", message="Structure charge")
 
+    # SpglibDataset warning introduced in v2.4.1
+    warnings.filterwarnings("ignore", message="dict interface")
+
 
 _ignore_pmg_warnings()
 

doped/core.py

@@ -29,6 +29,10 @@
 
     from easyunfold.procar import Procar as EasyunfoldProcar
 
+# SpglibDataset warning introduced in v2.4.1, can be ignored for now
+warnings.filterwarnings("ignore", message="dict interface")
+
+
 _orientational_degeneracy_warning = (
     "The defect supercell has been detected to possibly have a non-scalar matrix expansion, "
     "which could be breaking the cell periodicity and possibly preventing the correct _relaxed_ "
@@ -1364,7 +1368,10 @@ def _guess_and_set_struct_oxi_states(structure):
         if oxidation states could not be guessed.
     """
     bv_analyzer = BVAnalyzer()
-    with contextlib.suppress(ValueError):  # ValueError raised if oxi states can't be assigned
+    with contextlib.suppress(ValueError), warnings.catch_warnings():
+        # ValueError raised if oxi states can't be assigned, and SpglibDataset warning introduced in
+        # v2.4.1, can be ignored for now:
+        warnings.filterwarnings("ignore", message="dict interface")
         oxi_dec_structure = bv_analyzer.get_oxi_state_decorated_structure(structure)
         if all(
             np.isclose(int(specie.oxi_state), specie.oxi_state) for specie in oxi_dec_structure.species

doped/generation.py

@@ -1180,6 +1180,8 @@ class (such as ``clustering_tol``, ``stol``, ``min_dist`` etc), or to
 
             ``DefectsGenerator`` input parameters are also set as attributes.
         """
+        # SpglibDataset warning introduced in v2.4.1, can later remove when pymatgen updated to avoid this:
+        warnings.filterwarnings("ignore", message="dict interface")
         self.defects: dict[str, list[Defect]] = {}  # {defect_type: [Defect, ...]}
         self.defect_entries: dict[str, DefectEntry] = {}  # {defect_species: DefectEntry}
         self.structure = structure

doped/utils/symmetry.py

@@ -381,9 +381,9 @@ def get_wyckoff(frac_coords, struct, symm_ops: Optional[list] = None, equiv_site
     symm_dataset, unique_sites = _get_symm_dataset_of_struc_with_all_equiv_sites(
         frac_coords, struct, symm_ops, symprec=symprec
     )
-    conv_cell_factor = len(symm_dataset["std_positions"]) / len(symm_dataset["wyckoffs"])
+    conv_cell_factor = len(symm_dataset.std_positions) / len(symm_dataset.wyckoffs)
     multiplicity = int(conv_cell_factor * len(unique_sites))
-    wyckoff_label = f"{multiplicity}{symm_dataset['wyckoffs'][-1]}"
+    wyckoff_label = f"{multiplicity}{symm_dataset.wyckoffs[-1]}"
 
     return (wyckoff_label, unique_sites) if equiv_sites else wyckoff_label
 
@@ -1086,7 +1086,7 @@ def point_symmetry_from_defect(defect, symm_ops=None, symprec=0.01):
     symm_dataset, _unique_sites = _get_symm_dataset_of_struc_with_all_equiv_sites(
         defect.site.frac_coords, defect.structure, symm_ops=symm_ops, symprec=symprec
     )
-    spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["site_symmetry_symbols"][-1])
+    spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
     if spglib_point_group_symbol is not None:
         return spglib_point_group_symbol
 
@@ -1200,7 +1200,7 @@ def point_symmetry_from_defect_entry(
         # then easy, can just be taken from symmetry dataset of defect structure
         symm_dataset = _get_sga(defect_entry.defect.structure, symprec=symprec).get_symmetry_dataset()
         return schoenflies_from_hermann(
-            symm_dataset["site_symmetry_symbols"][defect_entry.defect.defect_site_index]
+            symm_dataset.site_symmetry_symbols[defect_entry.defect.defect_site_index]
         )
 
     supercell = _get_defect_supercell(defect_entry) if relaxed else _get_bulk_supercell(defect_entry)
@@ -1304,15 +1304,15 @@ def point_symmetry_from_defect_entry(
             # This issue is avoided for relaxed defect supercells as we take the symm_ops of our reduced
             # symmetry cell rather than that of the bulk (so no chance of spurious symmetry upgrade from
             # equivalent sites), and hence the max point symmetry is the point symmetry of the defect
-            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["site_symmetry_symbols"][-1])
+            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
 
             # Note that, if the supercell is non-periodicity-breaking, then the site symmetry can be simply
             # determined using the point group of the unrelaxed defect structure:
             # unrelaxed_defect_supercell = defect_entry.calculation_metadata.get(
             #     "unrelaxed_defect_structure", defect_supercell
             # )
             # return schoenflies_from_hermann(
-            #     _get_sga(unrelaxed_defect_supercell, symprec).get_symmetry_dataset()["pointgroup"],
+            #     _get_sga(unrelaxed_defect_supercell, symprec).get_symmetry_dataset().pointgroup,
             # )
             # But current approach works for all cases with unrelaxed defect structures
 
@@ -1321,15 +1321,15 @@ def point_symmetry_from_defect_entry(
             # the defect (e.g. for split-interstitials, split-vacancies, swapped vacancies etc),
             # so use 'pointgroup' output (in this case the reduced symmetry avoids the symmetry-upgrade
             # possibility with the equivalent sites, as when relaxed=False)
-            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["pointgroup"])
+            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.pointgroup)
 
             # This also works (at least for non-periodicity-breaking supercells) for relaxed defects in
             # most cases, but is slightly less robust (more sensitive to ``symprec`` choice) than the
             # approach above:
             # schoenflies_from_hermann(
             #     _get_sga(
             #         defect_supercell, symprec=symprec
-            #     ).get_symmetry_dataset()["pointgroup"]
+            #     ).get_symmetry_dataset().pointgroup
             # )
 
     if spglib_point_group_symbol is not None:
@@ -1376,7 +1376,7 @@ def _check_relaxed_defect_symmetry_determination(
 
     if unrelaxed_defect_structure is not None:
         unrelaxed_spglib_point_group_symbol = schoenflies_from_hermann(
-            _get_sga(unrelaxed_defect_structure, symprec=symprec).get_symmetry_dataset()["pointgroup"],
+            _get_sga(unrelaxed_defect_structure, symprec=symprec).get_symmetry_dataset().pointgroup,
         )
 
         bulk_supercell = _get_bulk_supercell(defect_entry)
@@ -1388,9 +1388,7 @@ def _check_relaxed_defect_symmetry_determination(
             symprec=symprec,
             dist_tol=symprec,
         )
-        bulk_spglib_point_group_symbol = schoenflies_from_hermann(
-            symm_dataset["site_symmetry_symbols"][-1]
-        )
+        bulk_spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
 
         if bulk_spglib_point_group_symbol != unrelaxed_spglib_point_group_symbol:
             if verbose: