Merge branch 'dev' of github.com:KrishnaswamyLab/graphtools into dev

KrishnaswamyLab · Jun 7, 2018 · 7422c97 · 7422c97
2 parents 96018b5 + 5b21471
commit 7422c97
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Showing 2 changed files with 2 additions and 14 deletions.
diff --git a/graphtools/api.py b/graphtools/api.py
@@ -201,7 +201,7 @@ def Graph(data,
     elif len(parent_classes) == 2:
         class Graph(parent_classes[0], parent_classes[1]):
             pass
-    elif len(parent_classes) == 2:
+    elif len(parent_classes) == 3:
         class Graph(parent_classes[0], parent_classes[1], parent_classes[2]):
             pass
     else:

diff --git a/graphtools/graphs.py b/graphtools/graphs.py
@@ -172,19 +172,7 @@ def build_kernel(self):
             symmetric matrix with ones down the diagonal
             with no non-negative entries.
         """
-        if self.decay is None or self.thresh == 1:
-            # binary connectivity matrix
-            # sklearn has a function for this
-            log_start("KNN search")
-            K = kneighbors_graph(self.knn_tree,
-                                 n_neighbors=self.knn,
-                                 metric=self.distance,
-                                 mode='connectivity',
-                                 include_self=True)
-            log_complete("KNN search")
-        else:
-            # sparse fast alpha decay
-            K = self.build_kernel_to_data(self.data_nu)
+        K = self.build_kernel_to_data(self.data_nu)
         # symmetrize
         K = (K + K.T) / 2
         return K