N clusters medoids fix (#129)

* Don't sample with replacement for random placement

You'll always have an inertia at least as good as not doing this; i.e.
picking distinct medoids only helps in the optimization.

* Add test to ensure n_clusters

It appears to only be the "random" initialization that has the bug, but
it's cheap to test all initializations + methods.

* The initial medoids changed for determinism

We're now sampling differently so the inital deterministic sample is
different. This updates the test to use the new deterministic medoids.

Author: stefanhannie

sklearn_extra/cluster/_k_medoids.py

@@ -412,7 +412,7 @@ def _initialize_medoids(self, D, n_clusters, random_state_):
 
         if self.init == "random":  # Random initialization
             # Pick random k medoids as the initial ones.
-            medoids = random_state_.choice(len(D), n_clusters)
+            medoids = random_state_.choice(len(D), n_clusters, replace=False)
         elif self.init == "k-medoids++":
             medoids = self._kpp_init(D, n_clusters, random_state_)
         elif self.init == "heuristic":  # Initialization by heuristic

sklearn_extra/cluster/tests/test_k_medoids.py

@@ -48,6 +48,24 @@ def test_kmedoid_results(method, init, dtype):
     assert dtype is np.dtype(km.transform(X_cc.astype(dtype)).dtype).type
 
 
+@pytest.mark.parametrize("method", ["alternate", "pam"])
+@pytest.mark.parametrize(
+    "init", ["random", "heuristic", "build", "k-medoids++"]
+)
+def test_kmedoid_nclusters(method, init):
+    n_clusters = 50
+
+    km = KMedoids(
+        n_clusters=n_clusters,
+        init=init,
+        method=method,
+        max_iter=1,
+        random_state=rng,
+    )
+    km.fit(X_cc)
+    assert len(np.unique(km.medoid_indices_)) == n_clusters
+
+
 def test_clara_results():
     expected = np.hstack([np.zeros(50), np.ones(50)])
     km = CLARA(n_clusters=2)
@@ -113,7 +131,7 @@ def test_random_deterministic():
     D = euclidean_distances(X)
 
     medoids = KMedoids(init="random")._initialize_medoids(D, 4, rng)
-    assert_array_equal(medoids, [47, 117, 67, 103])
+    assert_array_equal(medoids, [114, 62, 33, 107])
 
 
 def test_heuristic_deterministic():