Merge pull request #725 from xgi-org/remove-empty-edges

feat: add empties option to cleanup methods (#570)

Author: leotrs

tests/core/test_hypergraph.py

@@ -1000,3 +1000,22 @@ def test_cleanup():
     assert cleanH["name"] == "test"
 
     assert cleanH._edge == xgi.dual_dict(cleanH._node)
+
+
+def test_cleanup_empties():
+    """cleanup should remove empty edges by default and keep them with empties=True."""
+    H = xgi.Hypergraph([[1, 2, 3], [3, 4]])
+    H._edge[2] = set()
+    H._edge_attr[2] = {}
+    assert H.num_edges == 3
+    assert set(H.edges.empty()) == {2}
+
+    # default: remove empties
+    cleanH = H.cleanup(connected=False, relabel=False, in_place=False)
+    assert cleanH.num_edges == 2
+    assert set(cleanH.edges.empty()) == set()
+
+    # empties=True: keep them
+    cleanH = H.cleanup(connected=False, empties=True, relabel=False, in_place=False)
+    assert cleanH.num_edges == 3
+    assert set(cleanH.edges.empty()) == {2}

xgi/core/dihypergraph.py

@@ -1041,12 +1041,14 @@ def copy(self):
 
         return cp
 
-    def cleanup(self, isolates=False, relabel=True, in_place=True):
+    def cleanup(self, isolates=False, empties=False, relabel=True, in_place=True):
         if in_place:
             _DH = self
         else:
             _DH = self.copy()
 
+        if not empties:
+            _DH.remove_edges_from(_DH.edges.empty())
         if not isolates:
             _DH.remove_nodes_from(_DH.nodes.isolates())
         if relabel:

xgi/core/hypergraph.py

@@ -1469,6 +1469,7 @@ def cleanup(
         self,
         isolates=False,
         singletons=False,
+        empties=False,
         multiedges=False,
         connected=True,
         relabel=True,
@@ -1482,6 +1483,8 @@ def cleanup(
             Whether isolated nodes are allowed, by default False.
         singletons : bool, optional
             Whether singleton edges are allowed, by default False.
+        empties : bool, optional
+            Whether empty edges (edges with no nodes) are allowed, by default False.
         multiedges : bool, optional
             Whether multiedges are allowed, by default False.
         connected : bool, optional
@@ -1504,6 +1507,8 @@ def cleanup(
             _H.merge_duplicate_edges()
         if not singletons:
             _H.remove_edges_from(_H.edges.singletons())
+        if not empties:
+            _H.remove_edges_from(_H.edges.empty())
         if not isolates:
             _H.remove_nodes_from(_H.nodes.isolates())
         if connected:

xgi/core/simplicialcomplex.py

@@ -831,11 +831,15 @@ def copy(self):
 
         return cp
 
-    def cleanup(self, isolates=False, connected=True, relabel=True, in_place=True):
+    def cleanup(
+        self, isolates=False, empties=False, connected=True, relabel=True, in_place=True
+    ):
         if in_place:
             _S = self
         else:
             _S = self.copy()
+        if not empties:
+            _S.remove_simplex_ids_from(_S.edges.empty())
         if not isolates:
             _S.remove_nodes_from(_S.nodes.isolates())
         if connected: