fix for Scanpy sc.pp.neighbors backwards compatibility

dpeerlab · May 10, 2020 · eca0771 · eca0771
1 parent 63fd927
commit eca0771
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/src/harmony/core.py b/src/harmony/core.py
@@ -65,7 +65,11 @@ def augmented_affinity_matrix(
 
     temp = sc.AnnData(data_df.values)
     sc.pp.neighbors(temp, n_pcs=0, n_neighbors=n_neighbors)
-    kNN = temp.uns['neighbors']['distances']
+    # maintaining backwards compatibility to Scanpy `sc.pp.neighbors`
+    try:
+        kNN = temp.uns['neighbors']['distances']
+    except KeyError:
+        kNN = temp.obsp['distances']
 
     # Adaptive k
     adaptive_k = int(np.floor(n_neighbors / 3))

diff --git a/src/harmony/version.py b/src/harmony/version.py
@@ -1 +1 @@
-__version__ = "0.1.3"
+__version__ = "0.1.4"