MaterialsProjectCompatibility issue silencable deprecation warning (#…

…3017)

* MaterialsProjectCompatibility issue silencable deprecation warning

* SymmetrizedStructure type hints

pymatgen/core/lattice.py

@@ -971,17 +971,17 @@ def as_dict(self, verbosity: int = 0) -> dict:
             verbosity (int): Verbosity level. Default of 0 only includes the
                 matrix representation. Set to 1 for more details.
         """
-        d = {
+        dct = {
             "@module": type(self).__module__,
             "@class": type(self).__name__,
             "matrix": self._matrix.tolist(),
             "pbc": self._pbc,
         }
         if verbosity > 0:
             keys = ["a", "b", "c", "alpha", "beta", "gamma", "volume"]
-            d.update(dict(zip(keys, [*self.parameters, self.volume])))
+            dct.update(dict(zip(keys, [*self.parameters, self.volume])))
 
-        return d
+        return dct
 
     def find_all_mappings(
         self,

pymatgen/core/sites.py

@@ -599,13 +599,13 @@ def as_dict(self, verbosity: int = 0) -> dict:
         """
         species_list = []
         for spec, occu in self._species.items():
-            d = spec.as_dict()
-            del d["@module"]
-            del d["@class"]
-            d["occu"] = occu
-            species_list.append(d)
+            dct = spec.as_dict()
+            del dct["@module"]
+            del dct["@class"]
+            dct["occu"] = occu
+            species_list.append(dct)
 
-        d = {
+        dct = {
             "species": species_list,
             "abc": [float(c) for c in self._frac_coords],  # type: ignore
             "lattice": self._lattice.as_dict(verbosity=verbosity),
@@ -614,12 +614,12 @@ def as_dict(self, verbosity: int = 0) -> dict:
         }
 
         if verbosity > 0:
-            d["xyz"] = [float(c) for c in self.coords]
-            d["label"] = self.species_string
+            dct["xyz"] = [float(c) for c in self.coords]
+            dct["label"] = self.species_string
 
-        d["properties"] = self.properties
+        dct["properties"] = self.properties
 
-        return d
+        return dct
 
     @classmethod
     def from_dict(cls, d, lattice=None) -> PeriodicSite:

pymatgen/core/structure.py

@@ -2357,7 +2357,7 @@ def get_orderings(self, mode: Literal["enum", "sqs"] = "enum", **kwargs) -> list
             return [run_mcsqs(self, **kwargs).bestsqs]
         raise ValueError("Invalid mode!")
 
-    def as_dict(self, verbosity=1, fmt=None, **kwargs):
+    def as_dict(self, verbosity=1, fmt=None, **kwargs) -> dict[str, Any]:
         """
         Dict representation of Structure.
 
@@ -2386,21 +2386,21 @@ def as_dict(self, verbosity=1, fmt=None, **kwargs):
         latt_dict = self._lattice.as_dict(verbosity=verbosity)
         del latt_dict["@module"]
         del latt_dict["@class"]
-
-        d = {
+        sites = []
+        dct = {
             "@module": type(self).__module__,
             "@class": type(self).__name__,
             "charge": self.charge,
             "lattice": latt_dict,
-            "sites": [],
         }
         for site in self:
-            site_dict = site.as_dict(verbosity=verbosity)
+            site_dict = site.as_dict(verbosity=verbosity)  # type: ignore[call-arg]
             del site_dict["lattice"]
             del site_dict["@module"]
             del site_dict["@class"]
-            d["sites"].append(site_dict)
-        return d
+            sites.append(site_dict)
+        dct["sites"] = sites
+        return dct
 
     def as_dataframe(self):
         """

pymatgen/entries/compatibility.py

@@ -790,7 +790,13 @@ 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.
         """
+        warnings.warn(  # added by @janosh on 2023-05-25
+            "MaterialsProjectCompatibility is deprecated, Materials Project formation energies "
+            "use the newer MaterialsProject2020Compatibility scheme.",
+            DeprecationWarning,
+        )
         self.compat_type = compat_type
         self.correct_peroxide = correct_peroxide
         self.check_potcar_hash = check_potcar_hash

pymatgen/symmetry/structure.py

@@ -4,13 +4,16 @@
 
 from __future__ import annotations
 
-from typing import Sequence
+from typing import TYPE_CHECKING, Sequence
 
 import numpy as np
 from tabulate import tabulate
 
 from pymatgen.core.structure import PeriodicSite, Structure
 
+if TYPE_CHECKING:
+    from pymatgen.symmetry.analyzer import SpacegroupOperations
+
 
 class SymmetrizedStructure(Structure):
     """
@@ -27,17 +30,16 @@ class SymmetrizedStructure(Structure):
     def __init__(
         self,
         structure: Structure,
-        spacegroup,
+        spacegroup: SpacegroupOperations,
         equivalent_positions: Sequence[int],
         wyckoff_letters: Sequence[str],
-    ):
+    ) -> None:
         """
         Args:
             structure (Structure): Original structure
-            spacegroup (SpacegroupOperations): An input SpacegroupOperations from
-                SpacegroupAnalyzer.
-            equivalent_positions: Equivalent positions from SpacegroupAnalyzer.
-            wyckoff_letters: Wyckoff letters
+            spacegroup (SpacegroupOperations): An input SpacegroupOperations from SpacegroupAnalyzer.
+            equivalent_positions (list[int]): Equivalent positions from SpacegroupAnalyzer.
+            wyckoff_letters (list[str]): Wyckoff letters
         """
         self.spacegroup = spacegroup
         u, inv = np.unique(equivalent_positions, return_inverse=True)
@@ -73,13 +75,16 @@ def copy(self):
             wyckoff_letters=self.wyckoff_letters,
         )
 
-    def find_equivalent_sites(self, site) -> list[PeriodicSite]:
+    def find_equivalent_sites(self, site: PeriodicSite) -> list[PeriodicSite]:
         """
         Finds all symmetrically equivalent sites for a particular site
 
         Args:
             site (PeriodicSite): A site in the structure
 
+        Raises:
+            ValueError: if site is not in the structure.
+
         Returns:
             ([PeriodicSite]): List of all symmetrically equivalent sites.
         """
@@ -89,22 +94,22 @@ def find_equivalent_sites(self, site) -> list[PeriodicSite]:
 
         raise ValueError("Site not in structure")
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return str(self)
 
-    def __str__(self):
+    def __str__(self) -> str:
         outs = [
             "SymmetrizedStructure",
             f"Full Formula ({self.composition.formula})",
             f"Reduced Formula: {self.composition.reduced_formula}",
             f"Spacegroup: {self.spacegroup.int_symbol} ({self.spacegroup.int_number})",
         ]
 
-        def to_s(x):
+        def to_str(x):
             return f"{x:0.6f}"
 
-        outs.append("abc   : " + " ".join(to_s(i).rjust(10) for i in self.lattice.abc))
-        outs.append("angles: " + " ".join(to_s(i).rjust(10) for i in self.lattice.angles))
+        outs.append("abc   : " + " ".join(to_str(i).rjust(10) for i in self.lattice.abc))
+        outs.append("angles: " + " ".join(to_str(i).rjust(10) for i in self.lattice.angles))
         if self._charge:
             if self._charge >= 0:
                 outs.append(f"Overall Charge: +{self._charge}")
@@ -114,13 +119,13 @@ def to_s(x):
         data = []
         props = self.site_properties
         keys = sorted(props)
-        for i, sites in enumerate(self.equivalent_sites):
+        for idx, sites in enumerate(self.equivalent_sites):
             site = sites[0]
-            row = [str(i), site.species_string]
-            row.extend([to_s(j) for j in site.frac_coords])
-            row.append(self.wyckoff_symbols[i])
+            row = [str(idx), site.species_string]
+            row.extend([to_str(j) for j in site.frac_coords])
+            row.append(self.wyckoff_symbols[idx])
             for k in keys:
-                row.append(props[k][i])
+                row.append(props[k][idx])
             data.append(row)
         outs.append(
             tabulate(

pymatgen/symmetry/tests/test_analyzer.py

@@ -168,10 +168,9 @@ def test_get_refined_structure(self):
         refined_struct = sg.get_refined_structure(keep_site_properties=False)
         assert refined_struct.site_properties.get("magmom") is None
 
-    def test_get_symmetrized_structure(self):
+    def test_symmetrized_structure(self):
         symm_struct = self.sg.get_symmetrized_structure()
-        for a in symm_struct.lattice.angles:
-            assert a == 90
+        assert symm_struct.lattice.angles == (90, 90, 90)
         assert len(symm_struct.equivalent_sites) == 5
 
         symm_struct = self.disordered_sg.get_symmetrized_structure()
@@ -190,7 +189,7 @@ def test_get_symmetrized_structure(self):
 
         ss = SymmetrizedStructure.from_dict(d)
         assert ss.wyckoff_symbols[0] == "16h"
-        assert "SymmetrizedStructure" in str(ss)
+        assert str(ss).startswith("SymmetrizedStructure\nFull Formula (Li20.2 Ge2.06 P3.94 S24)\nReduced Formula: ")
 
     def test_find_primitive(self):
         """F m -3 m Li2O testing of converting to primitive cell."""