refactor: removing is_undirected from edge class definition

Not needed now since the branching is in ase/pymatgen routines now

matsciml/datasets/utils.py

@@ -607,12 +607,11 @@ def element_types():
 
 
 class Edge:
-    def __init__(
-        self, src: int, dst: int, image: np.ndarray, is_undirected: bool = False
-    ):
+    def __init__(self, src: int, dst: int, image: np.ndarray):
         """
         Initializes the Edge object with the source, destination,
         and image, ensuring directionality and handling self-loops.
+
         Parameters
         ----------
         src : int
@@ -622,17 +621,15 @@ def __init__(
         image : np.ndarray
             1D vector of three elements as a ``np.ndarray``.
         """
-        if is_undirected:
-            if src > dst:
-                # Enforce directed order
-                src, dst, image = dst, src, -image
+        if src > dst:
+            # Enforce directed order
+            src, dst, image = dst, src, -image
         if src == dst:
             # For self-loops, enforce a canonical form of the image
             image = self._canonicalize_image(image)
         self.src = src
         self.dst = dst
         self.image = image
-        self.is_undirected = is_undirected
 
     @staticmethod
     def _canonicalize_image(image: np.ndarray) -> np.ndarray:
@@ -686,10 +683,7 @@ def __eq__(self, other) -> bool:
         """
         if not isinstance(other, Edge):
             return False
-        if self.is_undirected:
-            node_eq = self.directed_index == other.directed_index
-        else:
-            node_eq = (self.src == other.src) and (self.dst == other.dst)
+        node_eq = self.directed_index == other.directed_index
         return node_eq and np.array_equal(self.image, other.image)
 
     def __str__(self) -> str:
@@ -865,7 +859,6 @@ def _all_sites_have_neighbors(neighbors):
                         src_idx,
                         site.index,
                         np.array(site.image),
-                        is_undirected,
                     )
                 )
         # now only keep the edges after the first loop
@@ -980,7 +973,7 @@ def calculate_ase_periodic_shifts(
         keep = set()
         # only keeps undirected edges that are unique
         for src, dst, image in zip(all_src, all_dst, all_images):
-            keep.add(Edge(src=src, dst=dst, image=image, is_undirected=is_undirected))
+            keep.add(Edge(src=src, dst=dst, image=image))
 
         all_src, all_dst, all_images = [], [], []
         num_atoms = len(atoms)