Implement a verbosity system and use the logging module

[mbelmadani]

Standard output (messages) writing is currently used inconsistently (for example, sometimes using sys.write(), others with print() ).

1. Every message or result specifc output (like the output pareto front, or motif statistics) should be using print() function. Other messages should use the python 'logging' module. Logger.info() for messages that are expected, Logger.critical() when the program errors and terminates, and Logger.warning( ) for anything else.

2. At the same time, add a check for a verbosity level for each Logger and print. Having the verbosity as a string would allow more flexibility to the user. An idea:

i = info
w = warning
s = stats
r = results
d = debug - Also print the source location of the message

The user provides a string with these tags (e.g. "isr" for everything except warnings) and logging is only done for those in the string. Critical level messages are always printed, unless there's a good reason not to.

Logger should be configured as:

import logging

if "l" in options.verbosity:
    FORMAT = '[%(filename)s:%(lineno)s - %(funcName)20s() ] %(asctime)15s - %(levelname)s : %(message)s'
else:
    FORMAT = '%(asctime)15s - %(levelname)s : %(message)s'
logging.basicConfig(format=FORMAT)
logger = logging.getLogger(__name__)

and messages logged with:

if` "w" in options.verbosity:
    logger.warning("The warning message")

This change should not be made for standalone scripts, this is only for motifgp.py and its classes.