Cleanup help message options parser

[XingerTang]

Goal

Add the -help option to the help message printout for consistent single hyphen option style.

Related discussions: AlphaGenes/AlphaPeel#237

Proposed approach

Change the relevant code as follows:

>>> import argparse
>>> parser = argparse.ArgumentParser(add_help=False)
>>> parser.add_argument('-h', '-help', '--help', help='display help message')
_StoreAction(option_strings=['-h', '-help', '--help'], dest='help', nargs=None, const=None, default=None, type=None, choices=None, required=False, help='display help message', metavar=None, deprecated=False)
>>> parser.print_help()
usage: [-h HELP]

options:
  -h, -help, --help HELP
                        display help message
>>> exit()

Scope

InputOutput.py

Done when

PR open by Apr 9th.