Remove deprecated (to|from|as|get)_string methods (#3561)

* Remove deprecated (to/from/as/get)_string methods

* refactor GaussianOutput.read_scan float conversion

* update test names and doc strings still saying (get/to)_string -> (get/to)_str

* fix doc str indent

* fix tests

* drop double @classmethod

pymatgen/alchemy/materials.py

@@ -11,7 +11,6 @@
 from typing import TYPE_CHECKING, Any
 from warnings import warn
 
-import numpy as np
 from monty.json import MSONable, jsanitize
 
 from pymatgen.core.structure import Structure
@@ -244,11 +243,6 @@ def structures(self) -> list[Structure]:
         h_structs = [Structure.from_dict(s["input_structure"]) for s in self.history if "input_structure" in s]
         return [*h_structs, self.final_structure]
 
-    @classmethod
-    @np.deprecate(message="Use from_cif_str instead")
-    def from_cif_string(cls, *args, **kwargs):  # noqa: D102
-        return cls.from_cif_str(*args, **kwargs)
-
     @classmethod
     def from_cif_str(
         cls,
@@ -295,11 +289,6 @@ def from_cif_str(
         }
         return cls(struct, transformations, history=[source_info])
 
-    @classmethod
-    @np.deprecate(message="Use from_poscar_str instead")
-    def from_poscar_string(cls, *args, **kwargs):  # noqa: D102
-        return cls.from_poscar_str(*args, **kwargs)
-
     @classmethod
     def from_poscar_str(
         cls, poscar_string: str, transformations: list[AbstractTransformation] | None = None

pymatgen/alchemy/transmuters.py

@@ -251,7 +251,7 @@ def __init__(self, cif_string, transformations=None, primitive=True, extend_coll
             if read_data:
                 structure_data[-1].append(line)
         for data in structure_data:
-            trafo_struct = TransformedStructure.from_cif_string("\n".join(data), [], primitive)
+            trafo_struct = TransformedStructure.from_cif_str("\n".join(data), [], primitive)
             transformed_structures.append(trafo_struct)
         super().__init__(transformed_structures, transformations, extend_collection)
 
@@ -291,7 +291,7 @@ def __init__(self, poscar_string, transformations=None, extend_collection=False)
             extend_collection: Whether to use more than one output structure
                 from one-to-many transformations.
         """
-        trafo_struct = TransformedStructure.from_poscar_string(poscar_string, [])
+        trafo_struct = TransformedStructure.from_poscar_str(poscar_string, [])
         super().__init__([trafo_struct], transformations, extend_collection=extend_collection)
 
     @staticmethod
@@ -309,7 +309,7 @@ def from_filenames(poscar_filenames, transformations=None, extend_collection=Fal
         trafo_structs = []
         for filename in poscar_filenames:
             with open(filename) as file:
-                trafo_structs.append(TransformedStructure.from_poscar_string(file.read(), []))
+                trafo_structs.append(TransformedStructure.from_poscar_str(file.read(), []))
         return StandardTransmuter(trafo_structs, transformations, extend_collection=extend_collection)
 
 

pymatgen/analysis/graphs.py

@@ -1251,7 +1251,7 @@ def __rmul__(self, other):
         return self.__mul__(other)
 
     @classmethod
-    def _edges_to_string(cls, g):
+    def _edges_to_str(cls, g):
         header = "from    to  to_image    "
         header_line = "----  ----  ------------"
         edge_weight_name = g.graph["edge_weight_name"]
@@ -1286,14 +1286,14 @@ def __str__(self):
         out = "Structure Graph"
         out += f"\nStructure: \n{self.structure}"
         out += f"\nGraph: {self.name}\n"
-        out += self._edges_to_string(self.graph)
+        out += self._edges_to_str(self.graph)
         return out
 
     def __repr__(self):
         s = "Structure Graph"
         s += f"\nStructure: \n{self.structure!r}"
         s += f"\nGraph: {self.name}\n"
-        s += self._edges_to_string(self.graph)
+        s += self._edges_to_str(self.graph)
         return s
 
     def __len__(self):
@@ -2608,7 +2608,7 @@ def from_dict(cls, dct):
         return cls(mol, dct["graphs"])
 
     @classmethod
-    def _edges_to_string(cls, g):
+    def _edges_to_str(cls, g):
         header = "from    to  to_image    "
         header_line = "----  ----  ------------"
         edge_weight_name = g.graph["edge_weight_name"]
@@ -2643,14 +2643,14 @@ def __str__(self) -> str:
         out = "Molecule Graph"
         out += f"\nMolecule: \n{self.molecule}"
         out += f"\nGraph: {self.name}\n"
-        out += self._edges_to_string(self.graph)
+        out += self._edges_to_str(self.graph)
         return out
 
     def __repr__(self) -> str:
         out = "Molecule Graph"
         out += f"\nMolecule: \n{self.molecule!r}"
         out += f"\nGraph: {self.name}\n"
-        out += self._edges_to_string(self.graph)
+        out += self._edges_to_str(self.graph)
         return out
 
     def __len__(self) -> int:

pymatgen/analysis/reaction_calculator.py

@@ -244,11 +244,6 @@ def from_dict(cls, d):
         products = {Composition(comp): coeff for comp, coeff in d["products"].items()}
         return cls(reactants, products)
 
-    @classmethod
-    @np.deprecate(message="Use from_str instead")
-    def from_string(cls, *args, **kwargs):
-        return cls.from_str(*args, **kwargs)
-
     @classmethod
     def from_str(cls, rxn_str):
         """

pymatgen/core/operations.py

@@ -411,10 +411,6 @@ def as_dict(self) -> dict[str, Any]:
             "tolerance": self.tol,
         }
 
-    @np.deprecate(message="Use as_xyz_str instead")
-    def as_xyz_string(self, *args, **kwargs):  # noqa: D102
-        return self.as_xyz_str(*args, **kwargs)
-
     def as_xyz_str(self) -> str:
         """Returns a string of the form 'x, y, z', '-x, -y, z', '-y+1/2, x+1/2, z+1/2', etc.
         Only works for integer rotation matrices.
@@ -425,11 +421,6 @@ def as_xyz_str(self) -> str:
 
         return transformation_to_string(self.rotation_matrix, translation_vec=self.translation_vector, delim=", ")
 
-    @classmethod
-    @np.deprecate(message="Use from_xyz_str instead")
-    def from_xyz_string(cls, *args, **kwargs):  # noqa: D102
-        return cls.from_xyz_str(*args, **kwargs)
-
     @classmethod
     def from_xyz_str(cls, xyz_str: str) -> SymmOp:
         """
@@ -501,7 +492,7 @@ def __eq__(self, other: object) -> bool:
         )
 
     def __str__(self) -> str:
-        return self.as_xyzt_string()
+        return self.as_xyzt_str()
 
     def __repr__(self) -> str:
         output = [
@@ -584,36 +575,27 @@ def from_rotation_and_translation_and_time_reversal(
         return MagSymmOp.from_symmop(symm_op, time_reversal)
 
     @classmethod
-    @np.deprecate(message="Use from_xyzt_str instead")
-    def from_xyzt_string(cls, *args, **kwargs):  # noqa: D102
-        return cls.from_xyzt_str(*args, **kwargs)
-
-    @classmethod
-    def from_xyzt_str(cls, xyzt_string: str) -> MagSymmOp:
+    def from_xyzt_str(cls, xyzt_str: str) -> MagSymmOp:
         """
         Args:
-            xyzt_string (str): of the form 'x, y, z, +1', '-x, -y, z, -1',
+            xyzt_str (str): of the form 'x, y, z, +1', '-x, -y, z, -1',
                 '-2y+1/2, 3x+1/2, z-y+1/2, +1', etc.
 
         Returns:
             MagSymmOp object
         """
-        symm_op = SymmOp.from_xyz_string(xyzt_string.rsplit(",", 1)[0])
+        symm_op = SymmOp.from_xyz_str(xyzt_str.rsplit(",", 1)[0])
         try:
-            time_reversal = int(xyzt_string.rsplit(",", 1)[1])
+            time_reversal = int(xyzt_str.rsplit(",", 1)[1])
         except Exception:
             raise Exception("Time reversal operator could not be parsed.")
         return cls.from_symmop(symm_op, time_reversal)
 
-    @np.deprecate(message="Use as_xyzt_str instead")
-    def as_xyzt_string(self, *args, **kwargs):  # noqa: D102
-        return self.as_xyzt_str(*args, **kwargs)
-
     def as_xyzt_str(self) -> str:
         """Returns a string of the form 'x, y, z, +1', '-x, -y, z, -1',
         '-y+1/2, x+1/2, z+1/2, +1', etc. Only works for integer rotation matrices.
         """
-        xyzt_string = SymmOp.as_xyz_string(self)
+        xyzt_string = SymmOp.as_xyz_str(self)
         return f"{xyzt_string}, {self.time_reversal:+}"
 
     def as_dict(self) -> dict[str, Any]:

pymatgen/core/periodic_table.py

@@ -1044,12 +1044,6 @@ def ionic_radius(self) -> float | None:
         warnings.warn(f"No ionic radius for {self}!")
         return None
 
-    @classmethod
-    @np.deprecate(message="Use from_str instead")
-    def from_string(cls, *args, **kwargs):
-        """Use from_str instead."""
-        return cls.from_str(*args, **kwargs)
-
     @classmethod
     def from_str(cls, species_string: str) -> Species:
         """Returns a Species from a string representation.

pymatgen/core/trajectory.py

@@ -397,7 +397,7 @@ def write_Xdatcar(
         """Writes to Xdatcar file.
 
         The supported kwargs are the same as those for the
-        Xdatcar_from_structs.get_string method and are passed through directly.
+        Xdatcar_from_structs.get_str method and are passed through directly.
 
         Args:
             filename: Name of file to write.  It's prudent to end the filename with

pymatgen/core/units.py

@@ -291,12 +291,6 @@ class FloatWithUnit(float):
 
     Error = UnitError
 
-    @classmethod
-    @np.deprecate(message="Use from_str instead")
-    def from_string(cls, *args, **kwargs):
-        """Use from_str instead."""
-        return cls.from_str(*args, **kwargs)
-
     @classmethod
     def from_str(cls, s):
         """Parse string to FloatWithUnit.

pymatgen/io/abinit/inputs.py

@@ -816,10 +816,6 @@ def _check_varname(self, key):
                 "Use Structure objects to prepare the input file."
             )
 
-    @np.deprecate(message="Use to_str instead")
-    def to_string(cls, *args, **kwargs):
-        return cls.to_str(*args, **kwargs)
-
     def to_str(self, post=None, with_structure=True, with_pseudos=True, exclude=None):
         """
         String representation.
@@ -1226,10 +1222,6 @@ def has_same_structures(self):
     def __str__(self):
         return self.to_str()
 
-    @np.deprecate(message="Use to_str instead")
-    def to_string(cls, *args, **kwargs):
-        return cls.to_str(*args, **kwargs)
-
     def to_str(self, with_pseudos=True):
         """
         String representation i.e. the input file read by Abinit.

pymatgen/io/abinit/netcdf.py

@@ -457,10 +457,6 @@ class AbinitHeader(AttrDict):
     def __str__(self):
         return self.to_str()
 
-    @np.deprecate(message="Use to_str instead")
-    def to_string(cls, *args, **kwargs):
-        return cls.to_str(*args, **kwargs)
-
     def to_str(self, verbose=0, title=None, **kwargs):
         """
         String representation. kwargs are passed to `pprint.pformat`.

pymatgen/io/abinit/pseudos.py

@@ -135,10 +135,6 @@ def __repr__(self) -> str:
     def __str__(self) -> str:
         return self.to_str()
 
-    @np.deprecate(message="Use to_str instead")
-    def to_string(cls, *args, **kwargs):
-        return cls.to_str(*args, **kwargs)
-
     def to_str(self, verbose=0) -> str:
         """String representation."""
 

pymatgen/io/adf.py

@@ -6,7 +6,6 @@
 import re
 from typing import TYPE_CHECKING
 
-import numpy as np
 from monty.io import reverse_readline
 from monty.itertools import chunks
 from monty.json import MSONable
@@ -333,11 +332,6 @@ def from_dict(cls, d):
         subkeys = [AdfKey.from_dict(k) for k in subkey_list] or None
         return cls(key, options, subkeys)
 
-    @classmethod
-    @np.deprecate(message="Use from_str instead")
-    def from_string(cls, *args, **kwargs):
-        return cls.from_str(*args, **kwargs)
-
     @classmethod
     def from_str(cls, string: str) -> AdfKey:
         """

pymatgen/io/atat.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import numpy as np
-from monty.dev import deprecated
 
 from pymatgen.core import Lattice, Structure, get_el_sp
 
@@ -28,10 +27,6 @@ def __init__(self, structure: Structure):
         """
         self.structure = structure
 
-    @deprecated(message="Use to_str instead")
-    def to_string(cls, *args, **kwargs):
-        return cls.to_str(*args, **kwargs)
-
     def to_str(self):
         """
         Returns:
@@ -59,10 +54,6 @@ def to_str(self):
 
         return "\n".join(output)
 
-    @deprecated(message="Use from_str instead")
-    def structure_from_string(cls, *args, **kwargs):
-        return cls.from_str(*args, **kwargs)
-
     @staticmethod
     def structure_from_str(data):
         """
@@ -134,7 +125,7 @@ def structure_from_str(data):
                     species_occ = [species_occ[0], 1.0]
 
                 if "_" in species_occ[0]:
-                    # see to_string() method in this file, since , and = are not valid
+                    # see to_str() method in this file, since , and = are not valid
                     # species names in AT-AT we replace "," with "__" and "=" with "___",
                     # for pymatgen to parse these back correctly we have to replace them back
                     species_occ[0] = species_occ[0].replace("___", "=").replace("__", ",")

pymatgen/io/babel.py

@@ -9,7 +9,6 @@
 import copy
 import warnings
 
-import numpy as np
 from monty.dev import requires
 
 from pymatgen.core.structure import IMolecule, Molecule
@@ -339,11 +338,6 @@ def from_molecule_graph(mol):
         """
         return BabelMolAdaptor(mol.molecule)
 
-    @classmethod
-    @np.deprecate(message="Use from_str instead")
-    def from_string(cls, *args, **kwargs):
-        return cls.from_str(*args, **kwargs)
-
     @needs_openbabel
     @classmethod
     def from_str(cls, string_data, file_format="xyz"):