old_contents: # -*- coding: utf-8 -*-
  
  import sys
  
  import click
  
  from indra.machine.utils import run_with_pmids_helper, run_with_search_helper, summarize_helper
  
  
  @click.group()
  def main():
      """The RAS Machine and utilities"""
  
  
  @main.command()
  @click.argument('model_path')
  @click.option('--config', help='Specify configuration file path, otherwise '
                                 'looks for config.yaml in model path')
  def run_with_search(model_path, config):
      """Run with PubMed search for new papers."""
      run_with_search_helper(model_path, config)
  
  
  @main.command()
  @click.argument('model_path')
  def summarize(model_path):
      """Print model summary."""
      summarize_helper(model_path)
  
  
  @main.command()
  @click.argument('model_path')
  @click.option('--pmids', type=click.File(), default=sys.stdin,
                help="A file with a PMID on each line")
  def run_with_pmids(model_path, pmids):
      """Run with given list of PMIDs."""
      run_with_pmids_helper(model_path, pmids)
  
  
  if __name__ == '__main__':
      main()
  
new_contents: # -*- coding: utf-8 -*-
  
  import sys
  
  import click
  
  
  @click.group()
  def machine():
      """The RAS Machine and utilities"""
  
  
  @machine.command()
  @click.argument('model_path')
  @click.option('--config', help='Specify configuration file path, otherwise '
                                 'looks for config.yaml in model path')
  def run_with_search(model_path, config):
      """Run with PubMed search for new papers."""
      from indra.machine.utils import run_with_search_helper
      run_with_search_helper(model_path, config)
  
  
  @machine.command()
  @click.argument('model_path')
  def summarize(model_path):
      """Print model summary."""
      from indra.machine.utils import summarize_helper
      summarize_helper(model_path)
  
  
  @machine.command()
  @click.argument('model_path')
  @click.option('--pmids', type=click.File(), default=sys.stdin,
                help="A file with a PMID on each line")
  def run_with_pmids(model_path, pmids):
      """Run with given list of PMIDs."""
      from indra.machine.utils import run_with_pmids_helper
      run_with_pmids_helper(model_path, pmids)
  
  
  if __name__ == '__main__':
      machine()
  
subject: Rename main to machine