refactor: unify and modernize periodic table utilities and typing

- Replace atomsymb and atommass tuples with AtomInfo dataclass and PTable enum for atomic data
- Refactor all usages to access atomic symbol and mass via PTable methods
- Remove nptyping dependency, switch to numpy.typing for type annotations
- Update molecule and atom classes to use new typing and atomic data access
- Bump numpy version to 2.x and remove nptyping from dependencies

diceplayer/environment/atom.py

@@ -1,52 +1,23 @@
-from diceplayer.utils.ptable import atommass
+from diceplayer.utils.ptable import PTable
+
+from dataclasses import dataclass
 
 
+@dataclass
 class Atom:
     """
     Atom class declaration. This class is used throughout the DicePlayer program to represent atoms.
-
-    Atributes:
-        lbl (int): Dice derived variable used to represent atoms with identical energies and simetric positions.
-        na (int): Atomic number of the represented atom.
-        rx (float): x cartesian coordinates of the represented atom.
-        ry (float): y cartesian coordinates of the represented atom.
-        rz (float): z cartesian coordinates of the represented atom.
-        chg (float): charge of the represented atom.
-        eps (float): quantum number epsilon of the represented atom.
-        sig (float): quantum number sigma of the represented atom.
     """
 
-    def __init__(
-        self,
-        lbl: int,
-        na: int,
-        rx: float,
-        ry: float,
-        rz: float,
-        chg: float,
-        eps: float,
-        sig: float,
-    ) -> None:
-        """
-        The constructor function __init__ is used to create new instances of the Atom class.
+    lbl: int
+    na: int
+    rx: float
+    ry: float
+    rz: float
+    chg: float
+    eps: float
+    sig: float
 
-        Args:
-            lbl (int): Dice derived variable used to represent atoms with identical energies and simetric positions.
-            na (int): Atomic number of the represented atom.
-            rx (float): x cartesian coordinates of the represented atom.
-            ry (float): y cartesian coordinates of the represented atom.
-            rz (float): z cartesian coordinates of the represented atom.
-            chg (float): charge of the represented atom.
-            eps (float): quantum number epsilon of the represented atom.
-            sig (float): quantum number sigma of the represented atom.
-        """
-
-        self.lbl = lbl
-        self.na = na
-        self.rx = rx
-        self.ry = ry
-        self.rz = rz
-        self.chg = chg
-        self.eps = eps
-        self.sig = sig
-        self.mass = atommass[self.na]
+    @property
+    def mass(self) -> float:
+        return PTable.get_atomic_mass(self.na)