for src_file, src_code in src_dict.iteritems():
  # assuming, here, that you want to honor the handle's path if already given
  filename = src_file.name
  if not "https://stackoverflow.com/" in filename:
    filename = os.path.join(filepath, filename)
  try:
    set.dependencies = subprocess.check_output(['unifdef', '-s', filename])
  except subprocess.CalledProcessError:
    pass # etc.
By the way, set is a bad variable name, since set is also a Python data type; you’re making the data type unusable in your code by shadowing it with a like-named variable. Don’t do that!
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solved cannot concatenate ‘str’ and ‘file’ objects : Python error