✨ set logger to debug; describe into column that leads to bad training

wfondrie · Oct 8, 2024 · c6089be · c6089be
1 parent 894a10c
commit c6089be
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Showing 3 changed files with 7 additions and 2 deletions.
diff --git a/mokapot/brew.py b/mokapot/brew.py
@@ -165,7 +165,7 @@ def brew(
             max_workers=max_workers,
         )
         for psms in train_psms:
-            LOGGER.info(psms.describe())
+            LOGGER.info(psms.NegLog10CombinePValue.describe())
         del train_sets
         fitted = Parallel(n_jobs=max_workers, require="sharedmem")(
             delayed(_fit_model)(d, datasets, copy.deepcopy(model), f)

diff --git a/mokapot/mokapot.py b/mokapot/mokapot.py
@@ -42,6 +42,8 @@ def main(main_args=None):
         level=verbosity_dict[config.verbosity],
     )
     logging.captureWarnings(True)
+    numba_logger = logging.getLogger('numba')
+    numba_logger.setLevel(logging.WARNING)
 
     # Suppress warning if asked for
     if config.suppress_warnings:

diff --git a/tests/system_tests/test_cli.py b/tests/system_tests/test_cli.py
@@ -1,3 +1,6 @@
+# tests/system_tests/test_cli.py
+
+
 """
 These tests verify that the CLI works as expected.
 
@@ -30,7 +33,7 @@ def phospho_files():
 
 def test_basic_cli(tmp_path, scope_files):
     """Test that basic cli works."""
-    params = [scope_files[0], "--dest_dir", tmp_path]
+    params = [scope_files[0], "--dest_dir", tmp_path, "--verbosity", 3]
     run_mokapot_cli(params)
     assert file_approx_len(tmp_path, "targets.psms.csv", 5487)
     assert file_approx_len(tmp_path, "targets.peptides.csv", 5183)