execute slow tests last

Author: oschwengers

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+addopts = --strict-markers
+markers =
+    slow: mark tests as slow.

test/conftest.py

@@ -0,0 +1,12 @@
+from _pytest.mark import Mark
+
+
+empty_mark = Mark('', [], {})
+
+
+def by_slow_marker(item):
+    return item.get_closest_marker('slow', default=empty_mark)
+
+
+def pytest_collection_modifyitems(items):
+    items.sort(key=by_slow_marker, reverse=False)

test/test_bakta.py

@@ -1,3 +1,5 @@
+import pytest
+
 from pathlib import Path
 from subprocess import run
 
@@ -14,6 +16,7 @@
 ]
 
 
+@pytest.mark.slow
 def test_bakta_mock_skipped_features(tmpdir):
     # fast test skipping all feature detections
     proc = run(["bin/bakta", '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', '--skip-tmrna', '--skip-trna', '--skip-rrna', '--skip-ncrna', '--skip-ncrna-region', '--skip-crispr', '--skip-cds', '--skip-sorf', '--skip-ori', '--skip-gap', 'test/data/NC_002127.1.fna'])
@@ -24,6 +27,7 @@ def test_bakta_mock_skipped_features(tmpdir):
         assert Path.exists(tmpdir_path.joinpath(file))
 
 
+@pytest.mark.slow
 def test_bakta_plasmid(tmpdir):
     # full test on plasmid
     proc = run(["bin/bakta", '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', 'test/data/NC_002127.1.fna'])
@@ -34,6 +38,7 @@ def test_bakta_plasmid(tmpdir):
         assert Path.exists(tmpdir_path.joinpath(file))
 
 
+@pytest.mark.slow
 def test_bakta_genome(tmpdir):
     # full test on plasmid
     proc = run(["bin/bakta", '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', 'test/data/GCF_000008865.2.fna.gz'])