rename __wrap_libsbml() parameters to avoid namespace collision; don'…

…t expect this to help circleCI run however

wc_lang/core.py

@@ -706,7 +706,7 @@ def add_to_sbml_doc(self, sbml_document):
             :obj:`LibSBMLError`: if calling `libsbml` raises an error
         """
         sbml_model = wrap_libsbml("sbml_document.getModel()")
-        wrap_libsbml("sbml_model.setIdAttribute({})".format(self.id))
+        wrap_libsbml("sbml_model.setIdAttribute('{}')".format(self.id))
         wrap_libsbml("sbml_model.setName(self.name)")
         # compartment, objective_function, and parameters are created separately
         if self.comments:

wc_lang/sbml/util.py

@@ -148,60 +148,60 @@ def _create_sbml_parameter(sbml_model, id, name=None, value=None, units=None, co
 create_sbml_unit = LibsbmlInterface._create_sbml_unit
 create_sbml_parameter = LibsbmlInterface._create_sbml_parameter
 
-def __wrap_libsbml(call, globals, locals, returns_int=False, debug=False):
+def __wrap_libsbml(_call, _globals, _locals, _returns_int=False, _debug=False):
     """ Wrap a libsbml method and properly handle errors.
 
     Unfortunately, libsbml methods that do not return data usually handle errors via return codes,
     instead of exceptions, and the generic return codes contain virtually no information.
     This function wraps these methods and raises useful exceptions when errors occur.
 
     Args:
-        call (:obj:`str`): a libsbml expression to execute
-        globals (:obj:`namespace`): the global namespace
-        locals (:obj:`namespace`): the local namespace at the calling code
-        returns_int (:obj:`bool`, optional): whether the method returns an int
-        debug (:obj:`bool`, optional): whether to print debug output
+        _call (:obj:`str`): a libsbml expression to execute
+        _globals (:obj:`namespace`): the global namespace
+        _locals (:obj:`namespace`): the local namespace at the calling code
+        _returns_int (:obj:`bool`, optional): whether the method returns an int
+        _debug (:obj:`bool`, optional): whether to print debug output
 
     Returns:
         :obj:`obj` or `int`: return the value returned by the libsbml method, either
         an object that has been created or retrieved, or an integer return code
 
     Raises:
-        :obj:`LibSBMLError`: if `call` contains an error, or the libsbml call returns None,
+        :obj:`LibSBMLError`: if `_call` contains an error, or the libsbml call returns None,
         or the libsbml call return a code != LIBSBML_OPERATION_SUCCESS
     """
-    if debug:
-        print('libsbml call:', call)
+    if _debug:
+        print('libsbml call:', _call)
     try:
-        rc = eval(call, globals, locals)
+        rc = eval(_call, _globals, _locals)
     except SyntaxError as error:
-        raise LibSBMLError("Syntax error in libsbml method call '{}'.".format(call))
+        raise LibSBMLError("Syntax error in libsbml method call '{}'.".format(_call))
     except NameError as error:
-        raise LibSBMLError("NameError '{}' in libsbml method call '{}'.".format(error, call))
+        raise LibSBMLError("NameError '{}' in libsbml method call '{}'.".format(error, _call))
     except Exception as error:
-        raise LibSBMLError("Error '{}' in libsbml method call '{}'.".format(error, call))
+        raise LibSBMLError("Error '{}' in libsbml method call '{}'.".format(error, _call))
     if rc == None:
-        raise LibSBMLError("libsbml returned None when executing '{}'.".format(call))
+        raise LibSBMLError("libsbml returned None when executing '{}'.".format(_call))
     elif type(rc) is int:
         if rc == LIBSBML_OPERATION_SUCCESS:
-            if debug:
+            if _debug:
                 print('libsbml returns: LIBSBML_OPERATION_SUCCESS')
             return rc
         else:
             error_code = OperationReturnValue_toString(rc)
             # Handle libsbml methods that return int as values
             # TODO: handle this more gracefully
-            if error_code is None or returns_int:
-                if debug:
+            if error_code is None or _returns_int:
+                if _debug:
                     print("libsbml returns:", rc)
                 return rc
             else:
                 raise LibSBMLError("LibSBML returned error code '{}' "
                     "when executing '{}'.\nWARNING: if the libsbml call above returns an int, then this "
-                    "error may be incorrect; pass 'returns_int=True' to wrap_libsbml().".format(error_code, call))
+                    "error may be incorrect; pass 'returns_int=True' to wrap_libsbml().".format(error_code, _call))
     else:
         # return data provided by libsbml method
-        if debug:
+        if _debug:
             print('libsbml returns:', rc)
         return rc