pytest: marked slow tests, full suite: 51 tests in 59 sec, fast: 40…

… tests in 13.7 sec

pyproject.toml

@@ -173,9 +173,13 @@ testpaths = [
   "tests",
 ]
 xfail_strict = true
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')"
+]
 addopts = [
     # "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
     "--import-mode=importlib",  # allow using test files with same name
+    "-m not slow",
 ]
 filterwarnings = [
     # "ignore:.*U.*mode is deprecated:DeprecationWarning",

tests/test_deseq2.py

@@ -1,8 +1,11 @@
+import pytest
+
 import pandas as pd
 
 from networkcommons._data.omics.deseq2 import deseq2
 
 
+@pytest.mark.slow
 def test_deseq2():
 
     # Create dummy dataset for testing, samples as colnames, genes as rownames

tests/test_node.py

@@ -53,6 +53,7 @@ def human_protein_ids() -> list[str]:
     return list(SAMPLE_HUMAN_PROTEINS.keys())
 
 
+@pytest.mark.slow
 def test_node_human_protein(human_protein_ids):
 
     for _id in human_protein_ids:
@@ -62,6 +63,7 @@ def test_node_human_protein(human_protein_ids):
         assert node.asdict() == SAMPLE_HUMAN_PROTEINS[_id]
 
 
+@pytest.mark.slow
 def test_node_id_translation(human_protein_ids):
 
     upc1_ensg = human_protein_ids[2]
@@ -73,13 +75,15 @@ def test_node_id_translation(human_protein_ids):
     assert list(upc1.as_idtype('uniprot'))[0].asdict() == upc1_uniprot_attrs
 
 
+@pytest.mark.slow
 def test_node_mouse_protein():
 
     egfr_m = _node.Node('Egfr', organism = 'mouse')
 
     assert egfr_m.asdict() == SAMPLE_MOUSE_PROTEINS['Egfr']
 
 
+@pytest.mark.slow
 def test_node_orthology_translation():
 
     egfr_m_o_attrs = SAMPLE_MOUSE_PROTEINS['Egfr'].copy()

tests/test_omics.py

@@ -28,6 +28,7 @@ def test_commons_url():
     assert 'metadata' in url
 
 
+@pytest.mark.slow
 def test_download(tmp_path):
 
     url = omics.common._commons_url('test', table = 'meta')
@@ -43,6 +44,7 @@ def test_download(tmp_path):
     assert line.startswith('sample_ID\t')
 
 
+@pytest.mark.slow
 def test_open():
 
     url = omics.common._commons_url('test', table = 'meta')
@@ -63,6 +65,7 @@ def test_open_df():
     assert df.shape == (4, 2)
 
 
+@pytest.mark.slow
 def test_decryptm_datasets():
 
     dsets = omics.decryptm.decryptm_datasets()
@@ -78,6 +81,7 @@ def decryptm_args():
     return 'KDAC_Inhibitors', 'Acetylome', 'curves_CUDC101.txt'
 
 
+@pytest.mark.slow
 def test_decryptm_table(decryptm_args):
 
     df = omics.decryptm.decryptm_table(*decryptm_args)
@@ -87,6 +91,7 @@ def test_decryptm_table(decryptm_args):
     assert df.EC50.dtype == 'float64'
 
 
+@pytest.mark.slow
 def test_decryptm_experiment(decryptm_args):
 
     dfs = omics.decryptm.decryptm_experiment(*decryptm_args[:2])
@@ -98,6 +103,7 @@ def test_decryptm_experiment(decryptm_args):
     assert dfs[3].EC50.dtype == 'float64'
 
 
+@pytest.mark.slow
 def test_panacea():
 
     dfs = omics.panacea()