text: import click
  import time
  from pathlib import Path
  
  from pysmFISH.logger_utils import selected_logger
  from pysmFISH.utils import create_dir
  
  from pysmFISH.configuration_files import create_general_analysis_config_file
  from pysmFISH.barcodes_analysis import simplify_barcodes_reference
  
  
  
  @click.group('processing_env')
  def setup_processing_env():
      """
      group of commands used to setup a processing env
      """
      pass
  
  @setup_processing_env.command('setup_de_novo_env')
  
  @click.option('--processing_folder_path', type=str, help='Path to the folder \
                  where the experiments will be processed')
  
  def de_novo_env(processing_folder_path:str):
      logger = selected_logger()
      click.echo('    ')
      click.echo('--------------------------------------------------------------')
      click.echo('Setup the requirements for the processing environment')
      click.echo('--------------------------------------------------------------')
      
      processing_folder_path = Path(processing_folder_path)
      config_path = processing_folder_path / 'config_db'
      codebooks_path = processing_folder_path / 'codebooks'
      probes_path = processing_folder_path / 'probes_sets'
      
      # Create the directories that will contain the files required for the processing
      create_dir(config_path)
      create_dir(codebooks_path)
      create_dir(probes_path)
  
      # Create the analysis master files
      create_general_analysis_config_file(config_path)
  
  
  @setup_processing_env.command('create_general_analysis_config')
  
  @click.option('--processing_folder_path', type=str, help='Path to the folder \
                  where the experiments will be processed')
  
  def recreate_general_analysis_config(processing_folder_path:str):
      logger = selected_logger()
      click.echo('    ')
      click.echo('--------------------------------------------------------------')
      click.echo('create general analysis config file')
      click.echo('--------------------------------------------------------------')
      
      processing_folder_path = Path(processing_folder_path)
  
      config_path = processing_folder_path / 'config_db'
  
      create_general_analysis_config_file(config_path)
  
  
  
  @setup_processing_env.command('convert_codebook')
  
  @click.option('--codebook_path', type=str, help='Path to the folder \
                  with the codebook to be parsed. The codebook excel file \
                  should be in the config_db folder')
  
  def convert_codebook(codebook_path:str):
      logger = selected_logger()
      click.echo('    ')
      click.echo('--------------------------------------------------------------')
      click.echo('Convert the codebook in a lighter version')
      click.echo('--------------------------------------------------------------')
      parser = simplify_barcodes_reference(codebook_path)
      parser.convert_barcode()
  