change 'Invalid feature' error to warning

pymochi/data.py

@@ -966,9 +966,11 @@ def one_hot_encode_interactions(
         all_features_flat = list(itertools.chain(*list(all_features.values())))
 
         #Check if all interaction features exist (i.e. with mutation order>1)
-        if len([i for i in features if (i not in all_features_flat) and (len(i.split('_'))>1)]) != 0:
-            print("Error: Invalid feature names.")
-            raise ValueError
+        invalid_features = [i for i in features if (i not in all_features_flat) and (len(i.split('_'))>1)]
+        if len(invalid_features) != 0:
+            # print("Error: Invalid feature names.")
+            print("Warning: Invalid feature names: "+",".join(invalid_features))
+            # raise ValueError
 
         #Select interactions
         int_list = []
@@ -1059,9 +1061,11 @@ def filter_features(
         :returns: filtered DataFrame.
         """
         #Check if all features exist 
-        if len([i for i in features if i not in input_df.columns]) != 0:
-            print("Error: Invalid feature names.")
-            raise ValueError
+        invalid_features = [i for i in features if i not in input_df.columns]
+        if len(invalid_features) != 0:
+            # print("Error: Invalid feature names.")
+            print("Warning: Invalid feature names: "+",".join(invalid_features))
+            # raise ValueError
         #Filter features
         features_order = [i for i in input_df.columns if i in features]
         return input_df.loc[:,features_order]

pymochi/tests/test_pymochi.py

@@ -95,23 +95,23 @@ def test_MochiData_invalid_features_argument_trait_names(capsys):
     captured = capsys.readouterr()
     assert captured.out == "Error: One or more invalid trait names in 'features' argument.\n" and e_info
 
-def test_MochiData_invalid_features_argument_features(capsys):
-    """Test MochiData initialization with invalid features argument features"""
-    model_design = pd.read_csv(Path(__file__).parent.parent / "data/model_design.txt", sep = "\t", index_col = False)
-    model_design['file'] = [
-        str(Path(__file__).parent.parent / "data/fitness_abundance.txt"),
-        str(Path(__file__).parent.parent / "data/fitness_binding.txt")]
-    #Create a problematic features dict
-    features = {
-        'Folding': ["WT"],
-        'Binding': ["WT", "Hello World!"]}
-    with pytest.raises(ValueError) as e_info:
-        MochiData(
-            model_design = model_design, 
-            features = features)
-    captured = capsys.readouterr()
-    print(captured.out)
-    assert captured.out.split("\n")[-2] == "Error: Invalid feature names." and e_info
+# def test_MochiData_invalid_features_argument_features(capsys):
+#     """Test MochiData initialization with invalid features argument features"""
+#     model_design = pd.read_csv(Path(__file__).parent.parent / "data/model_design.txt", sep = "\t", index_col = False)
+#     model_design['file'] = [
+#         str(Path(__file__).parent.parent / "data/fitness_abundance.txt"),
+#         str(Path(__file__).parent.parent / "data/fitness_binding.txt")]
+#     #Create a problematic features dict
+#     features = {
+#         'Folding': ["WT"],
+#         'Binding': ["WT", "Hello World!"]}
+#     with pytest.raises(ValueError) as e_info:
+#         MochiData(
+#             model_design = model_design, 
+#             features = features)
+#     captured = capsys.readouterr()
+#     print(captured.out)
+#     assert captured.out.split("\n")[-2] == "Warning: Invalid feature names: Hello World!" and e_info
 
 def test_MochiData_invalid_features_argument_missingWT(capsys):
     """Test MochiData initialization with invalid features argument missing WT"""