New recipe addressing #549 (#574)

* New recipe addressing #549

* Update recipes.ipynb

* response to review

tests/core/test_dihypergraph.py

@@ -722,6 +722,7 @@ def test_cleanup(dihypergraph1):
 
     # test relabel
     cleanDH = dihypergraph1.copy()
+    cleanDH["name"] = "test"
     cleanDH.cleanup()
     assert set(cleanDH.nodes) == {0, 1, 2, 3}
     assert cleanDH.num_edges == 3
@@ -735,3 +736,4 @@ def test_cleanup(dihypergraph1):
     edge_out = {i: e["out"] for i, e in cleanDH._edge.items()}
     assert edge_in == xgi.dual_dict(node_out)
     assert edge_out == xgi.dual_dict(node_in)
+    assert cleanDH["name"] == "test"

tests/core/test_hypergraph.py

@@ -948,11 +948,13 @@ def test_cleanup():
 
     # test relabel
     cleanH = H.copy()
+    cleanH["name"] = "test"
     cleanH.cleanup(connected=False)
     assert set(cleanH.nodes) == {0, 1, 2, 3, 4}
     assert cleanH.num_edges == 2
     edges = cleanH.edges.members()
     assert {0, 1, 2} in edges
     assert {3, 4} in edges
+    assert cleanH["name"] == "test"
 
     assert cleanH._edge == xgi.dual_dict(cleanH._node)

tests/core/test_simplicialcomplex.py

@@ -567,7 +567,9 @@ def test_cleanup():
 
     # test relabel
     cleanSC = SC.copy()
+    cleanSC["name"] = "test"
     cleanSC.cleanup(connected=False)
+    assert cleanSC["name"] == "test"
     assert set(cleanSC.nodes) == {0, 1, 2, 3, 4}
     assert cleanSC.num_edges == 5
     simplices = cleanSC.edges.members()

xgi/core/dihypergraph.py

@@ -978,14 +978,14 @@ def set_edge_attributes(self, values, name=None):
                     "dict-of-dicts has not been provided."
                 )
 
-    def clear(self, hypergraph_attr=True):
+    def clear(self, remove_net_attr=True):
         """Remove all nodes and edges from the graph.
 
         Also removes node and edge attributes, and optionally hypergraph attributes.
 
         Parameters
         ----------
-        hypergraph_attr : bool, optional
+        remove_net_attr : bool, optional
             Whether to remove hypergraph attributes as well.
             By default, True.
 
@@ -994,7 +994,7 @@ def clear(self, hypergraph_attr=True):
         self._node_attr.clear()
         self._edge.clear()
         self._edge_attr.clear()
-        if hypergraph_attr:
+        if remove_net_attr:
             self._net_attr.clear()
 
     def copy(self):

xgi/core/hypergraph.py

@@ -1195,14 +1195,14 @@ def update(self, *, edges=None, nodes=None):
         if edges:
             self.add_edges_from(edges)
 
-    def clear(self, hypergraph_attr=True):
+    def clear(self, remove_net_attr=True):
         """Remove all nodes and edges from the graph.
 
         Also removes node and edge attributes, and optionally hypergraph attributes.
 
         Parameters
         ----------
-        hypergraph_attr : bool, optional
+        remove_net_attr : bool, optional
             Whether to remove hypergraph attributes as well.
             By default, True.
 
@@ -1211,7 +1211,7 @@ def clear(self, hypergraph_attr=True):
         self._node_attr.clear()
         self._edge.clear()
         self._edge_attr.clear()
-        if hypergraph_attr:
+        if remove_net_attr:
             self._net_attr.clear()
 
     def clear_edges(self):
@@ -1467,7 +1467,6 @@ def cleanup(
             _H = self
         else:
             _H = self.copy()
-
         if not multiedges:
             _H.merge_duplicate_edges()
         if not singletons:

xgi/utils/utilities.py

@@ -408,7 +408,7 @@ def convert_labels_to_integers(net, label_attribute="label", in_place=False):
     node_attrs = net._node_attr.copy()
     edge_attrs = net._edge_attr.copy()
     edges = net._edge.copy()
-    net.clear()
+    net.clear(remove_net_attr=False)
     net.add_nodes_from((id, deepcopy(node_attrs[n])) for n, id in node_dict.items())
     net.set_node_attributes({id: {label_attribute: n} for n, id in node_dict.items()})
     if isinstance(net, SimplicialComplex):