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Improve bin calls

Jordi Inglada requested to merge improve_bin_calls into develop

All binary calls now go through a dedicated run function, which will do the appropriate logging:

def run(cmd, desc=None, env=os.environ)

desc is an optionnal string that is logged to INFO output to give a human readable description of the step corresponding to the call. Note that I did not update all calls to run() with a proper desc, this is mostly for future.

Feel free to comment on the choices I made (what goes where in logs ...)

Also, does the run method need to abort everything upon non-zero return code ? This can be added if needed.

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