bump coverage

graphtools/base.py

@@ -570,7 +570,7 @@ def _build_kernel(self):
         kernel = self.apply_anisotropy(kernel)
         if (kernel - kernel.T).max() > 1e-5:
             warnings.warn("K should be symmetric", RuntimeWarning)
-        if np.any(kernel.diagonal == 0):
+        if np.any(kernel.diagonal() == 0):
             warnings.warn("K should have a non-zero diagonal", RuntimeWarning)
         return kernel
 

test/test_exact.py

@@ -93,6 +93,11 @@ def test_precomputed_invalid():
         )
 
 
+def test_precomputed_nonzero_diagonal():
+    with assert_warns_message(RuntimeWarning, "K should have a non-zero diagonal"):
+        build_graph(np.zeros((10, 10)), precomputed="affinity", n_pca=None)
+
+
 def test_duplicate_data():
     with assert_warns_regex(
         RuntimeWarning,

test/test_knn.py

@@ -102,6 +102,14 @@ def test_knn_no_knn_no_bandwidth():
         build_graph(data, graphtype="knn", knn=None, bandwidth=None, thresh=1e-4)
 
 
+def test_knn_graph_invalid_symm():
+    with assert_raises_message(
+        ValueError,
+        "kernel_symm 'invalid' not recognized. Choose from '+', '*', 'mnn', or 'none'.",
+    ):
+        build_graph(data, graphtype="knn", knn=5, thresh=1e-4, kernel_symm="invalid")
+
+
 #####################################################
 # Check kernel
 #####################################################
@@ -152,6 +160,38 @@ def test_knn_graph():
         )
 
 
+def test_knn_graph_multiplication_symm():
+    k = 3
+    n_pca = 20
+    pca = PCA(n_pca, svd_solver="randomized", random_state=42).fit(data)
+    data_nu = pca.transform(data)
+    pdx = squareform(pdist(data_nu, metric="euclidean"))
+    knn_dist = np.partition(pdx, k, axis=1)[:, :k]
+    epsilon = np.max(knn_dist, axis=1)
+    K = np.empty_like(pdx)
+    for i in range(len(pdx)):
+        K[i, pdx[i, :] <= epsilon[i]] = 1
+        K[i, pdx[i, :] > epsilon[i]] = 0
+
+    W = K * K.T
+    np.fill_diagonal(W, 0)
+    G = pygsp.graphs.Graph(W)
+    G2 = build_graph(
+        data,
+        n_pca=n_pca,
+        decay=None,
+        knn=k - 1,
+        random_state=42,
+        use_pygsp=True,
+        kernel_symm="*",
+    )
+    assert G.N == G2.N
+    np.testing.assert_equal(G.dw, G2.dw)
+    assert (G.W - G2.W).nnz == 0
+    assert (G2.W - G.W).sum() == 0
+    assert isinstance(G2, graphtools.graphs.kNNGraph)
+
+
 def test_knn_graph_sparse():
     k = 3
     n_pca = 20

test/test_mnn.py

@@ -45,6 +45,10 @@ def test_sample_idx_unique():
         build_graph(
             data, graph_class=graphtools.graphs.MNNGraph, sample_idx=np.ones(len(data))
         )
+    with assert_warns_message(
+        UserWarning, "Only one unique sample. Not using MNNGraph"
+    ):
+        build_graph(data, sample_idx=np.ones(len(data)), graphtype="mnn")
 
 
 def test_sample_idx_none():

test/test_utils.py

@@ -33,3 +33,8 @@ def test_nonzero_discrete_knngraph(thresh):
 def test_nonzero_discrete_decay_graph(thresh):
     G = graphtools.Graph(data, n_pca=10, knn=5, decay=15, thresh=thresh)
     assert not graphtools.utils.nonzero_discrete(G.K, [0.5, 1])
+
+
+def test_nonzero_discrete_constant():
+    assert graphtools.utils.nonzero_discrete(2, [1, 2])
+    assert not graphtools.utils.nonzero_discrete(2, [1, 3])