Updated tests and pandas code

mokapot/model.py

@@ -512,7 +512,7 @@ def load_model(model_file):
         model.is_trained = True
 
     # Then try loading it with pickle:
-    except KeyError:
+    except (KeyError, UnicodeDecodeError):
         logging.info("Loading mokapot model.")
         with open(model_file, "rb") as mod_in:
             model = pickle.load(mod_in)

tests/system_tests/test_cli.py

@@ -9,6 +9,9 @@
 import pytest
 import pandas as pd
 
+# Warnings are errors for these tests
+pytestmark = pytest.mark.filterwarnings("error")
+
 
 @pytest.fixture
 def scope_files():
@@ -78,6 +81,20 @@ def test_cli_options(tmp_path, scope_files):
         tmp_path, f"blah.{file_bases[1]}.mokapot.peptides.txt"
     ).exists()
 
+    # Test keep_decoys:
+    assert Path(
+        tmp_path, f"blah.{file_bases[0]}.mokapot.decoy.psms.txt"
+    ).exists()
+    assert Path(
+        tmp_path, f"blah.{file_bases[0]}.mokapot.decoy.peptides.txt"
+    ).exists()
+    assert Path(
+        tmp_path, f"blah.{file_bases[1]}.mokapot.decoy.psms.txt"
+    ).exists()
+    assert Path(
+        tmp_path, f"blah.{file_bases[1]}.mokapot.decoy.peptides.txt"
+    ).exists()
+
 
 def test_cli_aggregate(tmp_path, scope_files):
     """Test that aggregate results in one result file."""