fix label handling during flatten

mbuild/compound.py

@@ -1917,6 +1917,9 @@ def flatten(self, inplace=True):
             for neighbor in nx.neighbors(bond_graph, particle):
                 new_bonds.append((particle, neighbor))
 
+        # Remove all labels which refer to children in the hierarchy
+        self.labels.clear()
+
         # Remove all the children
         if inplace:
             for child in children_list:

mbuild/tests/test_compound.py

@@ -801,42 +801,14 @@ def test_remove(self, ethane):
 
         # Test to reset labels after hydrogens
         ethane6 = mb.clone(ethane)
-        ethane6.flatten()
         hydrogens = ethane6.particles_by_name("H")
-        ethane6.remove(hydrogens)
+        ethane6.remove(hydrogens, reset_labels=True)
         assert list(ethane6.labels.keys()) == [
             "methyl1",
             "methyl2",
-            "C",
-            "C[0]",
-            "H",
-            "C[1]",
-            "port",
-            "port[1]",
-            "port[3]",
-            "port[5]",
-            "port[7]",
-            "port[9]",
-            "port[11]",
-        ]
-
-        ethane7 = mb.clone(ethane)
-        ethane7.flatten()
-        hydrogens = ethane7.particles_by_name("H")
-        ethane7.remove(hydrogens, reset_labels=True)
-
-        assert list(ethane7.labels.keys()) == [
-            "C",
-            "C[0]",
-            "C[1]",
-            "port",
-            "port[0]",
-            "port[1]",
-            "port[2]",
-            "port[3]",
-            "port[4]",
-            "port[5]",
         ]
+        assert ethane6.available_ports() == []
+        assert len(ethane6.all_ports()) == 6
 
     def test_remove_many(self, ethane):
         ethane.remove([ethane.children[0], ethane.children[1]])
@@ -1065,6 +1037,33 @@ def test_flatten_box_of_eth(self, ethane):
         box_of_eth.flatten()
         assert len(box_of_eth.children) == box_of_eth.n_particles == 8 * 2
         assert box_of_eth.n_bonds == 7 * 2
+        assert list(box_of_eth.labels.keys()) == [
+            "C",
+            "C[0]",
+            "H",
+            "H[0]",
+            "H[1]",
+            "H[2]",
+            "C[1]",
+            "H[3]",
+            "H[4]",
+            "H[5]",
+            "C[2]",
+            "H[6]",
+            "H[7]",
+            "H[8]",
+            "C[3]",
+            "H[9]",
+            "H[10]",
+            "H[11]",
+        ]
+
+    def test_flatten_then_fill_box(self, benzene):
+        benzene.flatten(inplace=True)
+        benzene_box = mb.packing.fill_box(
+            compound=benzene, n_compounds=2, density=0.3
+        )
+        assert next(iter(benzene_box.particles())).root.bond_graph
 
     def test_flatten_with_port(self, ethane):
         ethane.remove(ethane[2])