Address ruff's concerns.

Author: tsalo

Diff for: src/fmripost_aroma/utils/utils.py

@@ -116,7 +116,8 @@ def classification(features_df: pd.DataFrame):
 
     # Check the classifications
     is_motion = (features_df['csf_fract'] > THR_CSF) | (features_df['HFC'] > THR_HFC) | (proj > 0)
-    assert np.array_equal(is_motion, (clf_df['classification'] == 'rejected').values)
+    if not np.array_equal(is_motion, (clf_df['classification'] == 'rejected').values):
+        raise ValueError('Classification error: classifications do not match criteria.')
 
     # Remove trailing semicolons
     clf_df['rationale'] = clf_df['rationale'].str.rstrip(';')

Diff for: src/fmripost_aroma/workflows/aroma.py

@@ -532,7 +532,11 @@ def _select_melodic_files(melodic_dir):
     import os
 
     mixing = os.path.join(melodic_dir, 'melodic_mix')
-    assert os.path.isfile(mixing), f'Missing MELODIC mixing matrix: {mixing}'
+    if not os.path.isfile(mixing):
+        raise FileNotFoundError(f'Missing MELODIC mixing matrix: {mixing}')
+
     component_maps = os.path.join(melodic_dir, 'melodic_IC.nii.gz')
-    assert os.path.isfile(component_maps), f'Missing MELODIC ICs: {component_maps}'
+    if not os.path.isfile(component_maps):
+        raise FileNotFoundError(f'Missing MELODIC ICs: {component_maps}')
+
     return mixing, component_maps