tests for scperturb

tests/test_omics.py

@@ -1,6 +1,7 @@
 import pytest
 
 import pandas as pd
+import anndata as ad
 
 from networkcommons._data import omics
 
@@ -114,3 +115,39 @@ def test_panacea():
     assert dfs[0].shape == (24961, 1217)
     assert dfs[1].shape == (1216, 2)
     assert (dfs[0].drop('gene_symbol', axis = 1).dtypes == 'int64').all()
+
+
+@pytest.mark.slow
+def test_scperturb_metadata():
+
+    m = omics.scperturb_metadata()
+
+    assert isinstance(m, dict)
+    assert len(m['files']['entries']) == 50
+    assert m['versions'] == {'index': 4, 'is_latest': True}
+
+
+@pytest.mark.slow
+def test_scperturb_datasets():
+
+    example_url = (
+        'https://zenodo.org/api/records/10044268/files/'
+        'XuCao2023.h5ad/content'
+    )
+    dsets = omics.scperturb_datasets()
+
+    assert isinstance(dsets, dict)
+    assert len(dsets) == 50
+    assert dsets['XuCao2023.h5ad'] == example_url
+
+
+@pytest.mark.slow
+def test_scperturb():
+
+    var_cols = ('ensembl_id', 'ncounts', 'ncells')
+    adata = omics.scperturb('AdamsonWeissman2016_GSM2406675_10X001.h5ad')
+
+    assert isinstance(adata, ad.AnnData)
+    assert tuple(adata.var.columns) == var_cols
+    assert 'UMI count' in adata.obs.columns
+    assert adata.shape == (5768, 35635)