test for gamma/theta parameter confusion

graphtools/base.py

@@ -338,7 +338,16 @@ class BaseGraph(with_metaclass(abc.ABCMeta, Base)):
 
     def __init__(self, kernel_symm='+',
                  theta=None,
+                 gamma=None,
                  initialize=True, **kwargs):
+        if gamma is not None:
+            warnings.warn("gamma is deprecated. "
+                          "Setting theta={}".format(gamma), FutureWarning)
+            theta = gamma
+        if kernel_symm == 'gamma':
+            warnings.warn("kernel_symm='gamma' is deprecated. "
+                          "Setting kernel_symm='theta'", FutureWarning)
+            kernel_symm = 'theta'
         self.kernel_symm = kernel_symm
         self.theta = theta
         self._check_symmetrization(kernel_symm, theta)

test/test_mnn.py

@@ -10,6 +10,7 @@
     generate_swiss_roll,
     assert_raises,
     raises,
+    warns,
     cdist,
 )
 from scipy.linalg import norm
@@ -74,6 +75,26 @@ def test_mnn_with_vector_theta():
         theta=np.linspace(0, 1, n_sample - 1))
 
 
+@warns(FutureWarning)
+def test_mnn_with_gamma():
+    build_graph(
+        data, thresh=0, n_pca=20,
+        decay=10, knn=5, random_state=42,
+        sample_idx=digits['target'],
+        kernel_symm='theta',
+        gamma=0.9)
+
+
+@warns(FutureWarning)
+def test_mnn_with_kernel_symm_gamma():
+    build_graph(
+        data, thresh=0, n_pca=20,
+        decay=10, knn=5, random_state=42,
+        sample_idx=digits['target'],
+        kernel_symm='gamma',
+        theta=0.9)
+
+
 def test_mnn_with_non_zero_indexed_sample_idx():
     X, sample_idx = generate_swiss_roll()
     G = build_graph(X, sample_idx=sample_idx,