old_contents: import os
  
  import click
  import taca.log
  
  from pkg_resources import iter_entry_points
  
  from taca import __version__
  from taca.utils import config as conf
  
  
  @click.group()
  @click.version_option(__version__)
  # Priority for the configuration file is: environment variable > -c option > default
  @click.option('-c', '--config-file',
  			  default=os.path.join(os.environ['HOME'], '.taca/taca.yaml'),
  			  envvar='TACA_CONFIG',
  			  type=click.File('r'),
  			  help='Path to TACA configuration file')
  @click.pass_context
  def cli(ctx, config_file):
  	""" Tool for the Automation of Storage and Analyses """
  
  	ctx.obj = {}
  	config = conf.load_yaml_config(config_file)
  	log_file = config.get('log', {}).get('log_file', None)
  	if log_file:
  		level = config.get('log').get('log_level', 'INFO')
  		taca.log.init_logger_file(log_file, level)
  
  
  #Add subcommands dynamically to the CLI
  for entry_point in iter_entry_points('taca.subcommands'):
  	cli.add_command(entry_point.load())
  
new_contents: # -*- coding: utf-8 -*-
  import logging
  import os
  from pkg_resources import iter_entry_points
  
  import click
  import taca.log
  
  from taca import __version__
  from taca.utils import config as conf
  
  logger = logging.getLogger(__name__)
  
  
  @click.group()
  @click.version_option(__version__)
  # Priority for the configuration file is: environment variable > -c option > default
  @click.option('-c', '--config-file',
  			  default=os.path.join(os.environ['HOME'], '.taca/taca.yaml'),
  			  envvar='TACA_CONFIG',
  			  type=click.File('r'),
  			  help='Path to TACA configuration file')
  @click.pass_context
  def cli(ctx, config_file):
  	""" Tool for the Automation of Storage and Analyses """
  	ctx.obj = {}
  	config = conf.load_yaml_config(config_file)
  	log_file = config.get('log', {}).get('log_file', None)
  	if log_file:
  		level = config.get('log').get('log_level', 'INFO')
  		taca.log.init_logger_file(log_file, level)
  
  	logger.debug('starting up CLI')
  
  
  #Add subcommands dynamically to the CLI
  for entry_point in iter_entry_points('taca.subcommands'):
  	cli.add_command(entry_point.load())
  
subject: add initial logger to CLI this way you can easily see how it now works :-)