More suppression of (unnecessary) spglib deprecation warnings

doped/analysis.py

@@ -217,6 +217,7 @@ def defect_from_structures(
             Dictionary of bulk supercell Voronoi node information, for
             further expedited site-matching.
     """
+    warnings.filterwarnings("ignore", "dict interface")  # ignore spglib warning from v2.4.1
     try:
         def_type, comp_diff = get_defect_type_and_composition_diff(bulk_supercell, defect_supercell)
     except RuntimeError as exc:

doped/thermodynamics.py

@@ -230,6 +230,8 @@ def group_defects_by_distance(
     #  would be independent of this... but challenging to setup without complex clustering approaches (
     #  for now this works very well as is, and this is a rare case and usually not a problem anyway as
     #  dist_tol can just be adjusted as needed)
+    warnings.filterwarnings("ignore", "dict interface")  # ignore spglib warning from v2.4.1
+
     # initial group by Defect.name (same nominal defect), then distance to equiv sites
     # first make dictionary of nominal defect name: list of entries with that name
     defect_name_dict = {}

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
 
@@ -1182,6 +1182,7 @@ def point_symmetry_from_defect_entry(
         a boolean specifying if the supercell has been detected to break the crystal
         periodicity).
     """
+    warnings.filterwarnings("ignore", "dict interface")  # ignore spglib warning from v2.4.1
     if symprec is None:
         symprec = 0.1 if relaxed else 0.01  # relaxed structures likely have structural noise
         # May need to adjust symprec (e.g. for Ag2Se, symprec of 0.2 is too large as we have very
@@ -1200,7 +1201,7 @@ 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 +1305,15 @@ 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 +1322,15 @@ 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 +1377,7 @@ 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)
@@ -1388,7 +1389,9 @@ 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:
@@ -1485,6 +1488,7 @@ def point_symmetry(
         a boolean specifying if the supercell has been detected to break the crystal
         periodicity).
     """
+    warnings.filterwarnings("ignore", "dict interface")  # ignore spglib warning from v2.4.1
     if symprec is None:
         symprec = 0.1 if relaxed else 0.01  # relaxed structures likely have structural noise
 

tests/test_analysis.py

@@ -2127,7 +2127,9 @@ def test_extrinsic_interstitial_parsing_and_kumagai(self):
         # test symmetry determination (periodicity breaking does not affect F_i):
         with warnings.catch_warnings(record=True) as w:
             warnings.resetwarnings()
+            warnings.filterwarnings("ignore", "dict interface")  # ignore spglib warning from v2.4.1
             relaxed_defect_name = get_defect_name_from_entry(int_F_minus1_ent)
+            print([warn.message for warn in w])  # for debugging
             assert not w  # this supercell is not periodicity breaking
         assert relaxed_defect_name == "F_i_C4v_O2.67"
         assert get_defect_name_from_entry(int_F_minus1_ent, relaxed=False) == "F_i_Cs_O2.67"
@@ -2243,7 +2245,9 @@ def test_extrinsic_substitution_parsing_and_freysoldt_and_kumagai(self):
         # test symmetry determination (no warning here because periodicity breaking doesn't affect F_O):
         with warnings.catch_warnings(record=True) as w:
             warnings.resetwarnings()
+            warnings.filterwarnings("ignore", "dict interface")  # ignore spglib warning from v2.4.1
             relaxed_defect_name = get_defect_name_from_entry(F_O_1_ent)
+            print([warn.message for warn in w])  # for debugging
             assert len(w) == 0
         assert relaxed_defect_name == "F_O_D4h_Ti1.79"
         assert get_defect_name_from_entry(F_O_1_ent, relaxed=False) == "F_O_D4h_Ti1.79"

tests/test_generation.py

@@ -83,6 +83,8 @@ def _compare_attributes(obj1, obj2, exclude=None):
         elif attr == "defects" and any(len(i.defect_structure) == 0 for i in val1["vacancies"]):
             continue  # StructureMatcher comparison breaks for empty structures, which we can have with
             # our 1-atom primitive Cu input
+        elif isinstance(val1, (list, tuple)) and all(isinstance(i, np.ndarray) for i in val1):
+            assert all(np.array_equal(i, j) for i, j in zip(val1, val2)), "List of arrays do not match"
         else:
             assert val1 == val2
 

tests/test_vasp.py

@@ -4,7 +4,6 @@
 
 import contextlib
 import filecmp
-import json
 import locale
 import os
 import random
@@ -15,12 +14,11 @@
 import numpy as np
 import pytest
 from ase.build import bulk, make_supercell
-from monty.json import MontyEncoder
 from monty.serialization import loadfn
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.inputs import BadIncarWarning, Incar, Kpoints, Poscar, Potcar
-from test_generation import if_present_rm
+from test_generation import _compare_attributes, if_present_rm
 
 from doped.generation import DefectsGenerator
 from doped.vasp import (
@@ -1597,9 +1595,7 @@ def _check_reloaded_defect_entry(filename, ref_defect_entry):
                 reloaded_defect_entry.sc_defect_frac_coords,
                 ref_defect_entry.sc_defect_frac_coords,
             )
-            assert json.dumps(reloaded_defect_entry, sort_keys=True, cls=MontyEncoder) == json.dumps(
-                ref_defect_entry, sort_keys=True, cls=MontyEncoder
-            )
+            _compare_attributes(reloaded_defect_entry, ref_defect_entry)
 
         _check_reloaded_defect_entry("Ag_Sb_Cs_Te2.90_-2/vasp_std/Ag_Sb_Cs_Te2.90_-2.json", defect_entry)