From 174dc7b4c160a98920ffab2df7b64300496b676d Mon Sep 17 00:00:00 2001
From: Breno Freitas <brenolimadefreitas@gmail.com>
Date: Thu, 13 Jul 2017 21:33:08 -0400
Subject: [PATCH] Pass affinity to fix connectivity in linkage tree

Resolves #9308.
---
 sklearn/cluster/hierarchical.py            |  9 ++++----
 sklearn/cluster/tests/test_hierarchical.py | 27 ++++++++++++++++++++++
 2 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/sklearn/cluster/hierarchical.py b/sklearn/cluster/hierarchical.py
index 2195fe8ee3d85..59d8811cc728d 100644
--- a/sklearn/cluster/hierarchical.py
+++ b/sklearn/cluster/hierarchical.py
@@ -30,8 +30,7 @@
 # For non fully-connected graphs
 
 
-def _fix_connectivity(X, connectivity, n_components=None,
-                      affinity="euclidean"):
+def _fix_connectivity(X, connectivity, affinity):
     """
     Fixes the connectivity matrix
 
@@ -190,7 +189,8 @@ def ward_tree(X, connectivity=None, n_clusters=None, return_distance=False):
         else:
             return children_, 1, n_samples, None
 
-    connectivity, n_components = _fix_connectivity(X, connectivity)
+    connectivity, n_components = _fix_connectivity(X, connectivity,
+                                                   affinity='euclidean')
     if n_clusters is None:
         n_nodes = 2 * n_samples - 1
     else:
@@ -415,7 +415,8 @@ def linkage_tree(X, connectivity=None, n_components=None,
             return children_, 1, n_samples, None, distances
         return children_, 1, n_samples, None
 
-    connectivity, n_components = _fix_connectivity(X, connectivity)
+    connectivity, n_components = _fix_connectivity(X, connectivity,
+                                                   affinity=affinity)
 
     connectivity = connectivity.tocoo()
     # Put the diagonal to zero
diff --git a/sklearn/cluster/tests/test_hierarchical.py b/sklearn/cluster/tests/test_hierarchical.py
index 986b92e0ce9f4..f706966e8e80d 100644
--- a/sklearn/cluster/tests/test_hierarchical.py
+++ b/sklearn/cluster/tests/test_hierarchical.py
@@ -518,3 +518,30 @@ def test_agg_n_clusters():
         msg = ("n_clusters should be an integer greater than 0."
                " %s was provided." % str(agc.n_clusters))
         assert_raise_message(ValueError, msg, agc.fit, X)
+
+
+def test_affinity_passed_to_fix_connectivity():
+    # Test that the affinity parameter is actually passed to the pairwise
+    # function
+
+    size = 2
+    rng = np.random.RandomState(0)
+    X = rng.randn(size, size)
+    mask = np.array([True, False, False, True])
+
+    connectivity = grid_to_graph(n_x=size, n_y=size,
+                                 mask=mask, return_as=np.ndarray)
+
+    class FakeAffinity:
+        def __init__(self):
+            self.counter = 0
+
+        def increment(self, *args, **kwargs):
+            self.counter += 1
+            return self.counter
+
+    fa = FakeAffinity()
+
+    linkage_tree(X, connectivity=connectivity, affinity=fa.increment)
+
+    assert_equal(fa.counter, 3)