profile_simulation.py

import logging
log = logging.getLogger("main")
from optparse import OptionParser
import sys
from yeasty import config, script, context

cfg = config.Configuration(True)


def configure_options():
    usage = """usage: python %prog [options] <foldername>"""
    parser = OptionParser(usage)
    parser.add_option(
        "-v", "--verbose",
        action="store_true", dest="verbose",
        help="show verbose (debug) output")
    parser.add_option(
        "-c", "--clean",
        action="store_true", dest="clean",
        help="Clean any previous output")
    parser.add_option(
        "-g", "--graphics=",
        type="int", dest="graphics", default=0, metavar="N",
        help="show graphics every N steps")

    return parser


def configure_logging():
    # TODO Add additional logger in the output folder
    handler = logging.StreamHandler(sys.stdout)
    # format = "%(name)-15s | %(levelname)-8s | %(asctime)s | %(message)s"
    format = "%(name)-15s | %(levelname)-8s | %(message)s"
    formatter = logging.Formatter(format)
    handler.setFormatter(formatter)
    root = logging.getLogger("")
    root.addHandler(handler)
    root.setLevel(logging.INFO)


def load():
    global cfg
    configure_logging()
    parser = configure_options()
    options, args = parser.parse_args()
    ctx = context.Context(cfg)
    sct = script.Script(ctx)
    sct.load(args[0])


def run():
    global cfg
    cfg.experiment.run(None)

if __name__ == "__main__":
    import cProfile
    import pstats
    # Well behaved unix programs exits with 0 on success...
    load()
    cProfile.run('run()', 'profile.output')
    p = pstats.Stats('profile.output')
    p.sort_stats('time').print_stats(20)
    # p.strip_dirs().sort_stats(-1).print_stats()