Format test_pca.py

dwnorton · May 21, 2020 · 9811a08 · 9811a08
1 parent 535c102
commit 9811a08
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Showing 2 changed files with 33 additions and 24 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -47,7 +47,6 @@ exclude = '''
     )
     |tests/(
         test_get
-        |test_pca
         |test_neighbors
         |test_readwrite
         |test_clustering

diff --git a/scanpy/tests/test_pca.py b/scanpy/tests/test_pca.py
@@ -14,26 +14,30 @@
     [6, 0, 0, 2, 5],
     [0, 0, 0, 1, 0],
     [8, 8, 2, 1, 0],
-    [0, 0, 0, 4, 5]
+    [0, 0, 0, 4, 5],
 ]
 
-A_pca = np.array([
-    [-4.4783009 ,  5.55508466,  1.73111572, -0.06029139,  0.17292555],
-    [ 5.4855141 , -0.42651191, -0.74776055, -0.74532146,  0.74633582],
-    [ 0.01161428, -4.0156662 ,  2.37252748, -1.33122372, -0.29044446],
-    [-3.61934397,  0.48525412, -2.96861931, -1.16312545, -0.33230607],
-    [ 7.14050048,  1.86330409, -0.05786325,  1.25045782, -0.50213107],
-    [-4.53998399, -3.46146476, -0.32940009,  2.04950419,  0.20562023]
-])
-
-A_svd = np.array([
-    [-0.77034038, -2.00750922,  6.64603489, -0.39669256, -0.22212097],
-    [-9.47135856, -0.6326006 , -1.33787112, -0.24894361, -1.02044665],
-    [-5.90007339,  4.99658727,  0.70712592, -2.15188849,  0.30430008],
-    [-0.19132409,  0.42172251,  0.11169531,  0.50977966, -0.71637566],
-    [-11.1286238, -2.73045559,  0.08040596,  1.06850585,  0.74173764],
-    [-1.50180389,  5.56886849,  1.64034442,  2.24476032, -0.05109001]
-])
+A_pca = np.array(
+    [
+        [-4.4783009, 5.55508466, 1.73111572, -0.06029139, 0.17292555],
+        [5.4855141, -0.42651191, -0.74776055, -0.74532146, 0.74633582],
+        [0.01161428, -4.0156662, 2.37252748, -1.33122372, -0.29044446],
+        [-3.61934397, 0.48525412, -2.96861931, -1.16312545, -0.33230607],
+        [7.14050048, 1.86330409, -0.05786325, 1.25045782, -0.50213107],
+        [-4.53998399, -3.46146476, -0.32940009, 2.04950419, 0.20562023],
+    ]
+)
+
+A_svd = np.array(
+    [
+        [-0.77034038, -2.00750922, 6.64603489, -0.39669256, -0.22212097],
+        [-9.47135856, -0.6326006, -1.33787112, -0.24894361, -1.02044665],
+        [-5.90007339, 4.99658727, 0.70712592, -2.15188849, 0.30430008],
+        [-0.19132409, 0.42172251, 0.11169531, 0.50977966, -0.71637566],
+        [-11.1286238, -2.73045559, 0.08040596, 1.06850585, 0.74173764],
+        [-1.50180389, 5.56886849, 1.64034442, 2.24476032, -0.05109001],
+    ]
+)
 
 
 def test_pca_transform(array_type):
@@ -45,14 +49,20 @@ def test_pca_transform(array_type):
 
     sc.pp.pca(adata, n_comps=4, zero_center=True, svd_solver='arpack', dtype='float64')
 
-    assert np.linalg.norm(A_pca_abs[:, :4]-np.abs(adata.obsm['X_pca'])) < 2e-05
+    assert np.linalg.norm(A_pca_abs[:, :4] - np.abs(adata.obsm['X_pca'])) < 2e-05
 
-    sc.pp.pca(adata, n_comps=5, zero_center=True, svd_solver='randomized',
-              dtype='float64', random_state=14)
-    assert np.linalg.norm(A_pca_abs-np.abs(adata.obsm['X_pca'])) < 2e-05
+    sc.pp.pca(
+        adata,
+        n_comps=5,
+        zero_center=True,
+        svd_solver='randomized',
+        dtype='float64',
+        random_state=14,
+    )
+    assert np.linalg.norm(A_pca_abs - np.abs(adata.obsm['X_pca'])) < 2e-05
 
     sc.pp.pca(adata, n_comps=4, zero_center=False, dtype='float64', random_state=14)
-    assert np.linalg.norm(A_svd_abs[:, :4]-np.abs(adata.obsm['X_pca'])) < 2e-05
+    assert np.linalg.norm(A_svd_abs[:, :4] - np.abs(adata.obsm['X_pca'])) < 2e-05
 
 
 def test_pca_shapes():