changing assert statements to check arrays

scimap/tests/test_pp.py

@@ -45,11 +45,11 @@ def test_rescale (adata):
     from scimap.preprocessing.rescale import rescale
     manual_gate = pd.read_csv(os.getcwd() + '/scimap/tests/scimapExampleData/manual_gates.csv')
     adata = rescale (adata, gate=manual_gate)
-    assert round(adata.X[0][0], 2) == 0.12
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_rescale.npz')['data']
+    assert np.allclose(loaded_data, adata.X), "The arrays do not match."
 
-    np.testing.assert_allclose(adata.X[0][0], 0.11828568543672713)
 
-
 # combat
 def test_combat (adata):
     from scimap.preprocessing.combat import combat   
@@ -62,4 +62,10 @@ def test_combat (adata):
     adata = combat (adata, batch='ROI', layer='log', label='combat_log_layer')
     assert adata.layers['combat_log_layer'].shape == (11201, 9)
     adata = combat (adata, batch='ROI', replaceOriginal=True)
-    assert round(adata.X[0][0], 2) == 0.12
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_combat.npz')['data']
+    assert np.allclose(loaded_data, adata.X), "The arrays do not match."
+
+
+
+

scimap/tests/test_tl.py

@@ -10,6 +10,12 @@
 import os
 import anndata as ad
 import pandas as pd
+import numpy as np
+import pickle
+
+# def save_pickle(obj, filename): pickle.dump(obj, open(filename, 'wb'))
+#save_pickle(list(adata.obs['spatial_similarity_search_ROI2']), '/Users/aj/Dropbox (Partners HealthCare)/nirmal lab/softwares/scimap/scimap/tests/expected_test_values/test_spatial_similarity_search.pkl')
+load_pickle = lambda filename: pickle.load(open(filename, 'rb'))
 
 # load data
 @pytest.fixture
@@ -25,36 +31,47 @@ def test_phenotype (adata):
     # Load phenotype and test phenotyping
     phenotype = pd.read_csv(os. getcwd() + '/scimap/tests/scimapExampleData/phenotype_workflow.csv')
     adata = phenotype_cells (adata, phenotype=phenotype, gate = 0.5, label="phenotype")
-    assert adata.obs['phenotype'].iloc[0] == 'Immune'
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_phenotype.pkl')
+    assert loaded_data == list(adata.obs['phenotype']), "The lists do not match."
+
 
 #cluster
 def test_cluster (adata):
     from scimap.tools.cluster import cluster
     adata = cluster (adata,  method = 'kmeans', k= 5, use_raw = True)
-    assert adata.obs['kmeans'].value_counts().iloc[4] == 81
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_cluster.pkl')
+    assert loaded_data == list(adata.obs['kmeans']), "The lists do not match."
 
-
 #umap
 def test_umap (adata):
     from scimap.tools.umap import umap
     adata = umap(adata, label='umap_test')
-    assert adata.obsm['umap_test'].shape == (11201, 2)
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_umap.npz')['data']
+    assert np.allclose(loaded_data, adata.obsm['umap_test']), "The arrays do not match."
+    #assert adata.obsm['umap_test'].shape == (11201, 2)
 
 
 #foldchange
 def test_foldchange (adata):
     from scimap.tools.foldchange import foldchange
     adata = foldchange(adata, from_group = 'ROI1', imageid='ROI')
-    assert round(adata.uns['foldchange_fc']['Immune'], 2).values[0] == 1.87
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_foldchange.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['foldchange_fc'].to_numpy() ), "The arrays do not match."
 
 
 #spatial_distance
 def test_spatial_distance (adata):
     from scimap.tools.spatial_distance import spatial_distance
     adata = spatial_distance (adata)
-    assert round(adata.uns['spatial_distance']['Immune'].iloc[0], 2) == 521.27
-
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_distance.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_distance'].to_numpy()), "The arrays do not match."
 
+
 #spatial_interaction
 def test_spatial_interaction (adata):
     from scimap.tools.spatial_interaction import spatial_interaction
@@ -67,45 +84,68 @@ def test_spatial_interaction (adata):
 def test_spatial_count (adata):
     from scimap.tools.spatial_count import spatial_count
     adata = spatial_count (adata, phenotype='phenotype',method='knn',radius=5)
-    assert adata.uns['spatial_count'] is not None
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_count.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_count'].to_numpy()), "The arrays do not match."
 
     # test spatial cluster
     from scimap.tools.spatial_cluster import spatial_cluster
     adata = spatial_cluster(adata, df_name='spatial_count')
-    assert adata.obs['spatial_kmeans'].value_counts().iloc[3] == 1213
-
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_cluster.pkl')
+    assert loaded_data == list(adata.obs['spatial_kmeans']), "The lists do not match."
+
 
 #spatial_lda
 def test_spatial_lda (adata):
     from scimap.tools.spatial_lda import spatial_lda
     adata = spatial_lda (adata, num_motifs=10, radius=30)
-    assert round(adata.uns['spatial_lda']['Motif_0'].iloc[0], 3) == 0.05
+    assert adata.uns['spatial_lda'] is not None
 
 
 #spatial_expression
 def test_spatial_expression (adata):
     from scimap.tools.spatial_expression import spatial_expression
     adata = spatial_expression (adata, method='radius', radius=30, use_raw=True, label='spatial_expression')
-    assert round(adata.uns['spatial_expression']['ECAD'].sum(),0) == 81404.0
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_expression.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_expression'].to_numpy()), "The arrays do not match."
 
 
 #spatial_pscore
 def test_spatial_pscore (adata):
     from scimap.tools.spatial_pscore import spatial_pscore
     adata = spatial_pscore (adata,  proximity= ['Immune', 'ECAD+'])
-    assert adata.uns['spatial_pscore']['Immune_ECAD+'].values[0] == 2095
+    # load expected data
+    loaded_data = np.load( os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_pscore.npz')['data']
+    assert np.allclose(loaded_data, adata.uns['spatial_pscore'].to_numpy()), "The arrays do not match."
 
 
 #spatial_aggregate
 def test_spatial_aggregate (adata):
     from scimap.tools.spatial_aggregate import spatial_aggregate
     adata = spatial_aggregate (adata, purity = 60, phenotype='phenotype', method='knn', radius=10)
-    assert adata.obs['spatial_aggregate'].value_counts()['Immune'] == 3439
-
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_aggregate.pkl')
+    assert loaded_data == list(adata.obs['spatial_aggregate']), "The lists do not match."
+
 
 #spatial_similarity_search
 def test_spatial_similarity_search (adata):
     from scimap.tools.spatial_similarity_search import spatial_similarity_search
     adata = spatial_similarity_search (adata, ROI_column='ROI', similarity_threshold=0.6,  method='knn', radius=10)
-    assert adata.obs['spatial_similarity_search_ROI2'].value_counts()['similar_to_ROI'] == 4786
+    # load expected data
+    loaded_data = load_pickle(os.getcwd() + '/scimap/tests/expected_test_values/test_spatial_similarity_search.pkl')
+    assert loaded_data == list(adata.obs['spatial_similarity_search_ROI2']), "The lists do not match."
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