Switch error type and raise error when file missing

spras/analysis/ml.py

@@ -61,9 +61,8 @@ def summarize_networks(file_paths: Iterable[Union[str, PathLike]]) -> pd.DataFra
             p = PurePath(file)
             edge_tuples.append((p.parts[-2], edges))
 
-        except FileNotFoundError:
-            print(file, ' not found during ML analysis')  # should not hit this
-            continue
+        except FileNotFoundError as exc:
+            raise FileNotFoundError(str(file) + ' not found during ML analysis') from exc
 
     # initially construct separate dataframes per algorithm
     edge_dataframes = []
@@ -84,10 +83,10 @@ def summarize_networks(file_paths: Iterable[Union[str, PathLike]]) -> pd.DataFra
 
     # don't do ml post-processing if there is an empty dataframe or the number of samples is <= 1
     if concated_df.empty:
-        raise OSError("ML post-processing cannot proceed because the summarize network dataframe is empty.\nWe "
+        raise ValueError("ML post-processing cannot proceed because the summarize network dataframe is empty.\nWe "
                       "suggest setting ml include: false in the configuration file to avoid this error.")
     if min(concated_df.shape) <= 1:
-        raise OSError(f"ML post-processing cannot proceed because the available number of pathways is insufficient. "
+        raise ValueError(f"ML post-processing cannot proceed because the available number of pathways is insufficient. "
                       f"The ml post-processing requires more than one pathway, but currently "
                       f"there are only {min(concated_df.shape)} pathways.")
 

test/ml/test_ml.py

@@ -27,11 +27,11 @@ def test_summarize_networks(self):
         assert filecmp.cmp(OUT_DIR + 'dataframe.csv', EXPECT_DIR + 'expected-dataframe.csv', shallow=False)
 
     def test_summarize_networks_empty(self):
-        with pytest.raises(OSError): #raises error if empty dataframe is used for post processing
-            ml.summarize_networks([INPUT_DIR + 'test-data-empty/empty.txt'])
+        with pytest.raises(ValueError): #raises error if empty dataframe is used for post processing
+            ml.summarize_networks([INPUT_DIR + 'test-data-empty/emptya.txt'])
 
     def test_single_line(self):
-        with pytest.raises(OSError): #raises error if single line in file s.t. single row in dataframe is used for post processing
+        with pytest.raises(ValueError): #raises error if single line in file s.t. single row in dataframe is used for post processing
             ml.summarize_networks([INPUT_DIR + 'test-data-single/single.txt'])
 
     def test_pca(self):