Merge branch 'pr/3394' into master. Closes scipygh-2177.

See scipy#3394

Author: Ralf Gommers

scipy/cluster/hierarchy.py

@@ -795,8 +795,8 @@ def pre_order(self, func=(lambda x: x.id)):
         n = self.count
 
         curNode = [None] * (2 * n)
-        lvisited = np.zeros((2 * n,), dtype=bool)
-        rvisited = np.zeros((2 * n,), dtype=bool)
+        lvisited = set()
+        rvisited = set()
         curNode[0] = self
         k = 0
         preorder = []
@@ -807,13 +807,13 @@ def pre_order(self, func=(lambda x: x.id)):
                 preorder.append(func(nd))
                 k = k - 1
             else:
-                if not lvisited[ndid]:
+                if ndid not in lvisited:
                     curNode[k + 1] = nd.left
-                    lvisited[ndid] = True
+                    lvisited.add(ndid)
                     k = k + 1
-                elif not rvisited[ndid]:
+                elif ndid not in rvisited:
                     curNode[k + 1] = nd.right
-                    rvisited[ndid] = True
+                    rvisited.add(ndid)
                     k = k + 1
                 # If we've visited the left and right of this non-leaf
                 # node already, go up in the tree.

scipy/cluster/tests/test_hierarchy.py

@@ -813,6 +813,15 @@ def test_leaves_list_iris_average(self):
         node = to_tree(Z)
         self.assertTrue((node.pre_order() == leaves_list(Z)).all())
 
+    def test_iris_subtree_pre_order(self):
+        # Tests that pre_order() works when called on sub-trees.
+        X = eo['iris']
+        Y = pdist(X)
+        Z = linkage(X, 'single')
+        node = to_tree(Z)
+        self.assertTrue(node.pre_order() == (node.get_left().pre_order()
+                                             + node.get_right().pre_order()))
+
 
 class TestCorrespond(TestCase):
     def test_correspond_empty(self):