old_contents: """Configuration file for harness.py
  Author: Ian Huston
  
  """
  import logging
  import os.path
  
  
  ##############################
  # CHANGEABLE VALUES
  ##############################
  
  # Directory structure
  
  # Calculate base directory as being below $HOME
  CODEDIR = os.path.dirname(os.path.abspath(__package__))
  
  
  # Change the names of various directories
  CODEDIRNAME = "code"
  RUNDIRNAME = "runs"
  RESULTSDIRNAME = "results"
  LOGDIRNAME = "applogs"
  QSUBSCRIPTSDIRNAME = "qsubscripts"
  QSUBLOGSDIRNAME = "qsublogs"
  
  #Directory names computed from current code directory
  RUNDIR = os.path.dirname(CODEDIR)
  RESULTSDIR = os.path.join(RUNDIR, RESULTSDIRNAME)
  LOGDIR = os.path.join(RUNDIR, LOGDIRNAME)
  QSUBSCRIPTSDIR = os.path.join(RUNDIR, QSUBSCRIPTSDIRNAME)
  QSUBLOGSDIR = os.path.join(RUNDIR, QSUBLOGSDIRNAME)
  
  #Name of provenance file which records the code revisions and results files added
  provenancefilename = "provenance.log"
  
  # The logging level changes how much is saved to logging files. 
  # Choose from logging.DEBUG, .INFO, .WARN, .ERROR, .CRITICAL in decreasing order of verbosity
  LOGLEVEL = logging.INFO
  
  ##################################################
  # debug logging control
  # 0 for off, 1 for on
  # This can be changed using command line arguments
  ##################################################
  _debug = 1
  
  #Program name
  PROGRAM_NAME = "Pyflation"
  VERSION = "0.2"
  
new_contents: """Configuration file for harness.py
  Author: Ian Huston
  
  """
  import logging
  import os.path
  
  
  ##############################
  # CHANGEABLE VALUES
  ##############################
  
  # Directory structure
  
  # Calculate base directory as being below $HOME
  CODEDIR = os.path.dirname(os.path.abspath(__package__))
  
  
  # Change the names of various directories
  #Change to using the base run directory with bin, pyflation, scripts immediately below.
  CODEDIRNAME = "." 
  RUNDIRNAME = "runs"
  RESULTSDIRNAME = "results"
  LOGDIRNAME = "applogs"
  QSUBSCRIPTSDIRNAME = "qsubscripts"
  QSUBLOGSDIRNAME = "qsublogs"
  
  #Directory names computed from current code directory
  RUNDIR = CODEDIR
  RESULTSDIR = os.path.join(RUNDIR, RESULTSDIRNAME)
  LOGDIR = os.path.join(RUNDIR, LOGDIRNAME)
  QSUBSCRIPTSDIR = os.path.join(RUNDIR, QSUBSCRIPTSDIRNAME)
  QSUBLOGSDIR = os.path.join(RUNDIR, QSUBLOGSDIRNAME)
  
  #Name of provenance file which records the code revisions and results files added
  provenancefilename = "provenance.log"
  
  # The logging level changes how much is saved to logging files. 
  # Choose from logging.DEBUG, .INFO, .WARN, .ERROR, .CRITICAL in decreasing order of verbosity
  LOGLEVEL = logging.INFO
  
  ##################################################
  # debug logging control
  # 0 for off, 1 for on
  # This can be changed using command line arguments
  ##################################################
  _debug = 1
  
  #Program name
  PROGRAM_NAME = "Pyflation"
  VERSION = "0.2"
  
subject: Change directory structure so that pyflation, bin directory are directly below the top run directory e.g. runname |_ pyflation |_ bin |_ results |_ applogs etc.