old_contents: #! /usr/bin/python
  # -*- coding: utf-8 -*-
  
  import subprocess
  
  
  import logging
  logger = logging.getLogger(__name__)
  
  
  
  
  
  
  
  def update():
      # update submodules codes
      print ('Updating submodules')
      try:
          #import pdb; pdb.set_trace()
          subprocess.call('git pull', shell=True)
          subprocess.call('git submodule update --init --recursive', shell=True)
          subprocess.call('pip install -U --no-deps pysegbase --user', shell=True)
          subprocess.call('pip install -U --no-deps io3d --user', shell=True)
          subprocess.call('pip install -U --no-deps sed3 --user', shell=True)
          subprocess.call('pip install -U --no-deps skelet3d --user', shell=True)
      except:
          print ('Probem with git submodules')
  
  
  def main():
      logger = logging.getLogger()
  
      logger.setLevel(logging.WARNING)
      ch = logging.StreamHandler()
      logger.addHandler(ch)
      update()
                          
  if __name__ == "__main__":
      main()
  
new_contents: #! /usr/bin/python
  # -*- coding: utf-8 -*-
  
  import subprocess
  
  
  import logging
  logger = logging.getLogger(__name__)
  
  
  
  
  
  
  
  def update():
      # update submodules codes
      print ('Updating submodules')
      try:
          #import pdb; pdb.set_trace()
          subprocess.call('git pull', shell=True)
          subprocess.call('git submodule update --init --recursive', shell=True)
          subprocess.call('pip install -U --no-deps pysegbase --user', shell=True)
          subprocess.call('pip install -U --no-deps io3d --user', shell=True)
          subprocess.call('pip install -U --no-deps sed3 --user', shell=True)
  # skelet3d is not in pipy
          # subprocess.call('pip install -U --no-deps skelet3d --user', shell=True)
      except:
          print ('Probem with git submodules')
  
  
  def main():
      logger = logging.getLogger()
  
      logger.setLevel(logging.WARNING)
      ch = logging.StreamHandler()
      logger.addHandler(ch)
      update()
                          
  if __name__ == "__main__":
      main()
  
subject: fix skelet3d is not in pipy