pyneuroml/sbml/__init__.py now passing flake8 and black

pyneuroml/sbml/__init__.py

@@ -5,30 +5,30 @@
 
 import os
 import libsbml
-from libsbml import SBMLDocument, SBMLReader
+from libsbml import SBMLReader
+from typing import List
 
-def validate_sbml_files(input_files : str,units_consistency: bool = False):
-    '''
+
+def validate_sbml_files(input_files: str, units_consistency: bool = False):
+    """
     validate each input file using libsbml.SBMLDocument.checkConsistency
     input_files is a space separated list of one or more filepaths
-    '''
+    """
 
     for file_name in input_files.split():
         if not os.path.isfile(file_name):
-            raise OSError(
-                ("Could not find SBML file %s" % file_name)
-            )
+            raise OSError(("Could not find SBML file %s" % file_name))
 
         try:
             reader = SBMLReader()
             doc = reader.readSBML(file_name)
-        except:
-            raise OSError(
-                ("SBMLReader failed to load the file %s" % file_name)
-            )
+        except Exception:
+            raise OSError(("SBMLReader failed to load the file %s" % file_name))
 
         # set the unit checking, similar for the other settings
-        doc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, units_consistency)
+        doc.setConsistencyChecks(
+            libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, units_consistency
+        )
         doc.checkConsistency()
         # get errors/warnings
         n_errors: int = doc.getNumErrors()
@@ -61,4 +61,4 @@ def validate_sbml_files(input_files : str,units_consistency: bool = False):
                 print(
                     f"[{error.getSeverityAsString()}] {error.getShortMessage()} | {error.getMessage()}"
                 )
-        print("-" * 80)
+        print("-" * 80)

tests/sbml/test_sbml.py

@@ -2,5 +2,5 @@
 
 from pyneuroml import sbml
 
-fname = "test_data/test_doc.sbml"
+fname = "tests/sbml/test_data/test_doc.sbml"
 doc = sbml.validate_sbml_files(fname)