lots of from_string should be classmethod (#3177)

* `Incar.from_string` should be `classmethod`

* fix other `from_string`

Author: njzjz

pymatgen/core/units.py

@@ -309,6 +309,7 @@ class FloatWithUnit(float):
 
     Error = UnitError
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         """Use from_str instead."""

pymatgen/io/adf.py

@@ -354,6 +354,7 @@ 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)

pymatgen/io/babel.py

@@ -337,6 +337,7 @@ 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)

pymatgen/io/cif.py

@@ -165,6 +165,7 @@ def _process_string(cls, string):
                     q.append(tuple(s))
         return q
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
@@ -233,6 +234,7 @@ def __str__(self):
         out = "\n".join(map(str, self.data.values()))
         return f"{self.comment}\n{out}\n"
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)

pymatgen/io/cp2k/inputs.py

@@ -150,6 +150,7 @@ def from_dict(cls, d):
             verbose=d["verbose"],
         )
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
@@ -720,6 +721,7 @@ def from_file(file: str):
             txt = preprocessor(f.read(), os.path.dirname(f.name))
             return Cp2kInput.from_str(txt)
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
@@ -2247,6 +2249,7 @@ def softmatch(self, other):
         d2 = other.as_dict()
         return all(not (v is not None and v != d2[k]) for k, v in d1.items())
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
@@ -2551,6 +2554,7 @@ def softmatch(self, other):
         d2 = other.as_dict()
         return all(not (v is not None and v != d2[k]) for k, v in d1.items())
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
@@ -2692,6 +2696,7 @@ def get_string(self):
                 out += "\n"
         return out
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
@@ -2781,6 +2786,7 @@ def from_file(cls, fn):
                 obj.filename = fn
             return data
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)

pymatgen/io/exciting/inputs.py

@@ -73,6 +73,7 @@ def lockxyz(self):
     def lockxyz(self, lockxyz):
         self.structure.add_site_property("selective_dynamics", lockxyz)
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)

pymatgen/io/feff/inputs.py

@@ -278,6 +278,7 @@ def header_string_from_file(filename="feff.inp"):
 
         return "".join(feff_header_str)
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)

pymatgen/io/fiesta.py

@@ -554,6 +554,7 @@ def from_dict(cls, d):
             BSE_TDDFT_options=d["memory_options"],
         )
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)

pymatgen/io/gaussian.py

@@ -274,6 +274,7 @@ def _parse_species(sp_str):
 
         return Molecule(species, coords)
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)

pymatgen/io/lammps/inputs.py

@@ -521,6 +521,7 @@ def write_file(self, filename: str | Path, ignore_comments: bool = False, keep_s
         with zopen(filename, "wt") as f:
             f.write(self.get_string(ignore_comments=ignore_comments, keep_stages=keep_stages))
 
+    @classmethod
     @np.deprecate(message="Use from_str instead")
     def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)