From 0465530d651aa326a89f17e32243bfdbd15c6cbe Mon Sep 17 00:00:00 2001
From: deeenes <turei.denes@gmail.com>
Date: Tue, 2 Jul 2024 00:17:13 +0200
Subject: [PATCH] `pytest`: marked slow tests, full suite: 51 tests in 59 sec,
 fast: 40 tests in 13.7 sec

---
 pyproject.toml       | 4 ++++
 tests/test_deseq2.py | 3 +++
 tests/test_node.py   | 4 ++++
 tests/test_omics.py  | 6 ++++++
 4 files changed, 17 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index f538415..8c74176 100644
--- a/pyproject.toml
+++ b/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",
diff --git a/tests/test_deseq2.py b/tests/test_deseq2.py
index fb7228f..ccc07ff 100644
--- a/tests/test_deseq2.py
+++ b/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
diff --git a/tests/test_node.py b/tests/test_node.py
index 8a5dedc..c4d9ce6 100644
--- a/tests/test_node.py
+++ b/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]
@@ -73,6 +75,7 @@ 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')
@@ -80,6 +83,7 @@ def test_node_mouse_protein():
     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()
diff --git a/tests/test_omics.py b/tests/test_omics.py
index d19af3a..9c1dae2 100644
--- a/tests/test_omics.py
+++ b/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()