Log execution time for stages

[sacdallago]

From a management perspective, being able to log how long a stage executes for is useful information (undoubtably for the web, but even for fair share on o2 etc.).

This would translate in a function in utils/pipeline.py that gets called at the beginning and end (suppose you only run one stage and want logging on how long that took) of this for loop https://github.com/debbiemarkslab/EVcouplings/blob/develop/evcouplings/utils/pipeline.py#L141 . This is obviously optional, I'd add a key in management, called report_execution_time that may be not set or False for no reporting, and only if explicitly set to True will report said execution time.

I think #166 is already way too feature packed to put this in as well, so I'm gonna do this once that PR is merged.