Replace some deprecated API (#4228)

* TO BE REVERTED: mark spglib deprecation as error

* filter known deprecation warning

* replace some deprecated API

* revert debug filter

* set deprecation warning as error

* MaterialsProjectCompatibility -> MaterialsProject2020Compatibility

* remove non-existent arg

* filter known warning

* fix grammar

* revert warning filter

---------

Co-authored-by: Shyue Ping Ong <[email protected]>

Author: DanielYang59

src/pymatgen/command_line/critic2_caller.py

@@ -766,7 +766,7 @@ def get_volume_and_charge(nonequiv_idx):
     def _parse_stdout(self, stdout):
         warnings.warn(
             "Parsing critic2 standard output is deprecated and will not be maintained, "
-            "please use the native JSON output in future.",
+            "please use the native JSON output in the future.",
             DeprecationWarning,
             stacklevel=2,
         )

src/pymatgen/entries/compatibility.py

@@ -913,7 +913,6 @@ def __init__(
             correct_peroxide: Specify whether peroxide/superoxide/ozonide
                 corrections are to be applied or not.
             check_potcar_hash (bool): Use potcar hash to verify potcars are correct.
-            silence_deprecation (bool): Silence deprecation warning. Defaults to False.
         """
         self.compat_type = compat_type
         self.correct_peroxide = correct_peroxide

src/pymatgen/io/feff/inputs.py

@@ -190,8 +190,8 @@ def __init__(
             self.periodic = True
             sym = SpacegroupAnalyzer(struct, **self.spacegroup_analyzer_settings)
             data = sym.get_symmetry_dataset()
-            self.space_number = data.get("number")
-            self.space_group = data.get("international")
+            self.space_number = data.number
+            self.space_group = data.international
         # for Molecule, skip the symmetry check
         elif isinstance(self.struct, Molecule):
             self.periodic = False

tests/electronic_structure/test_boltztrap2.py

@@ -80,6 +80,7 @@ def test_get_volume(self):
         assert self.loader.get_volume() == approx(477.6256714925874, abs=1e-5)
 
 
+@pytest.mark.filterwarnings("ignore:BandstructureLoader is deprecated:DeprecationWarning")
 class TestBandstructureLoader(TestCase):
     def setUp(self):
         self.loader = BandstructureLoader(BAND_STRUCT, VASP_RUN.structures[-1])
@@ -107,6 +108,7 @@ def test_set_upper_lower_bands(self):
         assert self.loader_sp_dn.ebands.shape == (14, 198)
 
 
+@pytest.mark.filterwarnings("ignore:VasprunLoader is deprecated:DeprecationWarning")
 class TestVasprunLoader(TestCase):
     def setUp(self):
         self.loader = VasprunLoader(VASP_RUN)

tests/entries/test_computed_entries.py

@@ -470,11 +470,11 @@ def setUp(self):
             for temp in self.temps
         }
 
-        with open(f"{TEST_DIR}/Mn-O_entries.json") as file:
-            data = json.load(file)
         with open(f"{TEST_DIR}/structure_CO2.json") as file:
             self.co2_struct = MontyDecoder().process_decoded(json.load(file))
 
+        with open(f"{TEST_DIR}/Mn-O_entries.json") as file:
+            data = json.load(file)
         self.mp_entries = [MontyDecoder().process_decoded(d) for d in data]
 
     def test_gf_sisso(self):

tests/ext/test_matproj.py

@@ -908,7 +908,7 @@ def test_parity_with_mp_api(self):
             pytest.skip("mp_api.client.MPRester cannot be imported for this test.")
         mpr_mp_api = MpApi(PMG_MAPI_KEY)
         # Test summary
-        mp_data = mpr_mp_api.summary.search(formula="Al2O3")
+        mp_data = mpr_mp_api.materials.search(formula="Al2O3")
         pmg_data = self.rester.get_summary({"formula": "Al2O3"})
         assert len(mp_data) == len(pmg_data)