[Breaking/Fix] Skip isotopes when iterating through core.Element (#…

…4180)

* try to overwrite iter

* add test

* enhance module documentation, remove ptable class

* also check full members

* also check full members

* inherit from EnumType

* avoid hard-coding isotopes

* revert to enummeta

* add named_isotopes property

* fix incorrect merge

---------

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

src/pymatgen/core/periodic_table.py

@@ -1,4 +1,9 @@
-"""Classes representing Element, Species (Element + oxidation state) and PeriodicTable."""
+"""Classes representing:
+- Element: Element in the periodic table.
+- Species: Element with optional oxidation state and spin.
+- DummySpecies: Non-traditional Elements/Species (vacancies/...).
+- ElementType: element types (metal/noble_gas/halogen/s_block/...).
+"""
 
 from __future__ import annotations
 
@@ -8,7 +13,7 @@
 import re
 import warnings
 from collections import Counter
-from enum import Enum, unique
+from enum import Enum, EnumMeta, unique
 from itertools import combinations, product
 from pathlib import Path
 from typing import TYPE_CHECKING, overload
@@ -864,7 +869,20 @@ def print_periodic_table(filter_function: Callable | None = None) -> None:
             print(" ".join(row_str))
 
 
-class Element(ElementBase):
+class _ElementMeta(EnumMeta):
+    """Override Element to handle isotopes."""
+
+    def __iter__(cls):
+        """Skip named isotopes when iterating."""
+        return (elem for elem in super().__iter__() if not elem._is_named_isotope)
+
+    @property
+    def named_isotopes(cls):
+        """Get all named isotopes."""
+        return tuple(elem for elem in super().__iter__() if elem._is_named_isotope)
+
+
+class Element(ElementBase, metaclass=_ElementMeta):
     """Enum representing an element in the periodic table."""
 
     # This name = value convention is redundant and dumb, but unfortunately is

tests/core/test_periodic_table.py

@@ -29,6 +29,25 @@ def test_init(self):
 
         assert id(Element("Fe")) == id(Element("Fe"))  # Test caching
 
+    def test_iter(self):
+        # Make sure isotopes don't show during iteration
+        assert [elem.name for elem in Element] == (
+            "H,He,Li,Be,B,C,N,O,F,Ne,Na,Mg,Al,Si,P,S,Cl,Ar,K,Ca,Sc,Ti,V,Cr,"
+            "Mn,Fe,Co,Ni,Cu,Zn,Ga,Ge,As,Se,Br,Kr,Rb,Sr,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,"
+            "Ag,Cd,In,Sn,Sb,Te,I,Xe,Cs,Ba,La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,"
+            "Yb,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi,Po,At,Rn,Fr,Ra,Ac,Th,Pa,U,Np,"
+            "Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr,Rf,Db,Sg,Bh,Hs,Mt,Ds,Rg,Cn,Nh,Fl,Mc,Lv,Ts,Og"
+        ).split(",")
+
+        # Make sure isotopes are still in members
+        assert list(Element.__members__) == (
+            "H,D,T,He,Li,Be,B,C,N,O,F,Ne,Na,Mg,Al,Si,P,S,Cl,Ar,K,Ca,Sc,Ti,V,Cr,"
+            "Mn,Fe,Co,Ni,Cu,Zn,Ga,Ge,As,Se,Br,Kr,Rb,Sr,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,"
+            "Ag,Cd,In,Sn,Sb,Te,I,Xe,Cs,Ba,La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,"
+            "Yb,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi,Po,At,Rn,Fr,Ra,Ac,Th,Pa,U,Np,"
+            "Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr,Rf,Db,Sg,Bh,Hs,Mt,Ds,Rg,Cn,Nh,Fl,Mc,Lv,Ts,Og"
+        ).split(",")
+
     def test_missing_and_confusing_data(self):
         with pytest.warns(UserWarning, match="No data available"):
             _ = Element.H.metallic_radius
@@ -391,6 +410,8 @@ def test_isotope(self):
             3.0155007134,
         ]
 
+        assert Element.named_isotopes == (Element.D, Element.T)
+
 
 class TestSpecies(PymatgenTest):
     def setUp(self):