old_contents: #!/usr/bin/env python
  #
  # @file    deviser.py
  # @brief   command line tool for invoking the deviser scripts
  # @author  Frank Bergmann
  # @author  Sarah Keating
  #
  # <!--------------------------------------------------------------------------
  #
  # Copyright (c) 2013-2014 by the California Institute of Technology
  # (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
  # and the University of Heidelberg (Germany), with support from the National
  # Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
  #
  # Permission is hereby granted, free of charge, to any person obtaining a
  # copy of this software and associated documentation files (the "Software"),
  # to deal in the Software without restriction, including without limitation
  # the rights to use, copy, modify, merge, publish, distribute, sublicense,
  # and/or sell copies of the Software, and to permit persons to whom the
  # Software is furnished to do so, subject to the following conditions:
  #
  # The above copyright notice and this permission notice shall be included in
  # all copies or substantial portions of the Software.
  #
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  #
  # Neither the name of the California Institute of Technology (Caltech), nor
  # of the European Bioinformatics Institute (EMBL-EBI), nor of the University
  # of Heidelberg, nor the names of any contributors, may be used to endorse
  # or promote products derived from this software without specific prior
  # written permission.
  # ------------------------------------------------------------------------ -->
  #
  
  
  import sys
  
  from util import generateLatex
  from legacy import run
  
  
  def generatePackageFor(filename): 
      """This function generates a libSBML extension for the given filename"""
      run.generatePackageForFile(filename)
  
  
  def generateLaTeXFor(filename):
      """This function generates a LaTeX scaffold for the given filename"""
      generateLatex.generateLatexFor(filename)
  
  
  def main(args):
      """Usage: deviser  [--generate | --latex ] input-filename output-dir
         This program will use a Deviser xml file, and generate either a C++
         libSBML extionsion for it, or generate a LaTeX scaffold for its
         specification.
      """
  
      if len(args) != 3:
          print(main.__doc__)
          sys.exit(1)
  
      operation = args[1].lower()
      filename = args[2]
    
      if operation == '--generate' or operation == '-g':
          generatePackageFor(filename)
      elif operation == '--latex' or operation == '-l':
          generateLaTeXFor(filename)
      else:
          print(main.__doc__)
          sys.exit(1)
  
      return 0
    
  if __name__ == '__main__':
      main(sys.argv)
  
new_contents: #!/usr/bin/env python
  #
  # @file    deviser.py
  # @brief   command line tool for invoking the deviser scripts
  # @author  Frank Bergmann
  # @author  Sarah Keating
  #
  # <!--------------------------------------------------------------------------
  #
  # Copyright (c) 2013-2014 by the California Institute of Technology
  # (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
  # and the University of Heidelberg (Germany), with support from the National
  # Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
  #
  # Permission is hereby granted, free of charge, to any person obtaining a
  # copy of this software and associated documentation files (the "Software"),
  # to deal in the Software without restriction, including without limitation
  # the rights to use, copy, modify, merge, publish, distribute, sublicense,
  # and/or sell copies of the Software, and to permit persons to whom the
  # Software is furnished to do so, subject to the following conditions:
  #
  # The above copyright notice and this permission notice shall be included in
  # all copies or substantial portions of the Software.
  #
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  #
  # Neither the name of the California Institute of Technology (Caltech), nor
  # of the European Bioinformatics Institute (EMBL-EBI), nor of the University
  # of Heidelberg, nor the names of any contributors, may be used to endorse
  # or promote products derived from this software without specific prior
  # written permission.
  # ------------------------------------------------------------------------ -->
  #
  
  
  import sys
  
  from util import generateLatex, generateCode
  from legacy import run
  
  
  def generatePackageFor(filename):
      """This function generates a libSBML extension for the given filename"""
      generateCode.generate_code_for(filename, True)
  
  
  def generateLegacyPackageFor(filename):
      """This function generates a libSBML extension for the given filename
         using the legacy code"""
      run.generatePackageForFile(filename)
  
  
  def generateLaTeXFor(filename):
      """This function generates a LaTeX scaffold for the given filename"""
      generateLatex.generateLatexFor(filename)
  
  
  def main(args):
      """Usage: deviser  [--generate | --latex ] input-filename output-dir
         This program will use a Deviser xml file, and generate either a C++
         libSBML extionsion for it, or generate a LaTeX scaffold for its
         specification.
      """
  
      if len(args) != 3:
          print(main.__doc__)
          sys.exit(1)
  
      operation = args[1].lower()
      filename = args[2]
    
      if operation == '--legacy' or operation == '-gl':
          generateLegacyPackageFor(filename)
      if operation == '--generate' or operation == '-g':
          generatePackageFor(filename)
      elif operation == '--latex' or operation == '-l':
          generateLaTeXFor(filename)
      else:
          print(main.__doc__)
          sys.exit(1)
  
      return 0
    
  if __name__ == '__main__':
      main(sys.argv)
  
subject: use new code