change test_data

tests/test_basic.py

@@ -1,23 +1,23 @@
-from scvelo.tools.velocity_graph import *
-from scvelo.tools.solver import *
-from scvelo.tools.velocity_embedding import transition_matrix
+import scvelo as scv
+import scanpy.api as sc
 
-from anndata import AnnData
-from scanpy.api.pp import normalize_per_cell, pca, neighbors
-from time import time
-from scipy import sparse, stats
+from scvelo.tools.utils import *
 
 
 def test_data(n_obs=100, n_vars=10):
-    adata = AnnData(sparse.random(n_obs, n_vars, data_rvs=stats.poisson(1).rvs, density=.6, format='csr'))
-    adata.layers['spliced'] = adata.X
-    adata.layers['unspliced'] = \
-        .5 * adata.X + .3 * sparse.random(n_obs, n_vars, density=.6, data_rvs=stats.poisson(1).rvs, format='csr')
-
-    normalize_per_cell(adata, layers='all')
-    pca(adata)
-    neighbors(adata, use_rep='X_pca')
-    moments(adata)
+    if False:
+        adata = AnnData(sparse.random(n_obs, n_vars, data_rvs=stats.poisson(1).rvs, density=.6, format='csr'))
+        adata.layers['spliced'] = adata.X
+        adata.layers['unspliced'] = \
+           .5 * adata.X + .3 * sparse.random(n_obs, n_vars, density=.6, data_rvs=stats.poisson(1).rvs, format='csr')
+
+    adata = scv.datasets.dentategyrus()
+    sc.pp.filter_genes(adata, min_counts=10)
+    sc.pp.filter_genes_dispersion(adata)
+    sc.pp.normalize_per_cell(adata, layers='all')
+    sc.pp.pca(adata)
+    sc.pp.neighbors(adata, use_rep='X_pca')
+    scv.pp.moments(adata)
     return adata
 
 
@@ -28,43 +28,16 @@ def test_einsum():
     assert np.allclose(prod_sum_var(Ms, Mu), np.sum(Ms * Mu, 1))
     assert np.allclose(norm(Ms), np.linalg.norm(Ms, axis=1))
 
-    start = time()
-
-    prod_sum_obs(Ms, Mu)
-    stop1 = time()
-
-    np.sum(Ms * Mu, 0)
-    stop2 = time()
-
-    print('einsum product is ', round((stop2 - start) / (stop1 - start), 2), ' times faster than numpy.')
-
-    start = time()
-
-    norm(Ms)
-    stop1 = time()
-
-    np.linalg.norm(Ms, axis=1)
-    stop2 = time()
-
-    print('einsum norm is ', round((stop2 - start) / (stop1 - start), 2), ' times faster than numpy.')
-
-
-# def test_solvers():
-#     adata = test_data()
-#     Ms, Mu = adata.layers['Ms'], adata.layers['Mu']
-#
-#     assert np.allclose(solve_cov(Ms, Mu), solve_inv(Ms, Mu))
-
 
 def test_velocity_graph():
     adata = test_data()
-    velocity(adata)
-    velocity_graph(adata)
+    scv.tl.velocity(adata)
+    scv.tl.velocity_graph(adata)
 
     graph1 = adata.uns['velocity_graph'].copy()
 
-    velocity_graph(adata, n_jobs=2)
+    scv.tl.velocity_graph(adata, n_jobs=2)
     graph2 = adata.uns['velocity_graph'].copy()
 
-    assert np.allclose((transition_matrix(adata) > 0).toarray(), (graph1 > 0).toarray())
+    assert np.allclose((scv.tl.transition_matrix(adata) > 0).toarray(), (graph1 > 0).toarray())
     assert np.allclose(graph1.toarray(), graph2.toarray())