def main():
parser = get_minimal_parser()
# add configuration specific to this tool.
parser.description = dedent("""
Run CADET simulator for a given input HDF5 file.
""")
parser.add_argument(
'input_file',
default=None,
help='The name of the h5 file containing CADET inputs to run CADET on.'
)
args = parser.parse_args()
if not isabs(args.log_dir):
log_dir = join(args.output_dir, args.log_dir)
else:
log_dir = args.log_dir
initialize_logging('run-cadet-sim',
verbose=args.verbose,
log_file=args.log,
log_dir=log_dir)
run_cadet_simulator(args.input_file)
def test_setuplogging_with_file(self):
log_file = abspath(join(HERE, "temp.log"))
initialize_logging(log_file=log_file)
try:
self.assert_log_file_found(expected_file=log_file)
finally:
attempt_remove_file(log_file)
def test_setuplogging_with_prefix(self):
initialize_logging(prefix="TEMP")
try:
self.assert_log_file_found()
finally:
log_file = get_log_file()
attempt_remove_file(log_file)
def main():
parser = get_minimal_parser()
# add configuration specific to this tool.
parser.description = dedent("""
Run Chromatography simulation for a given experiment.
The experiment data is read from the provided excel file.
""")
parser.add_argument(
'input_file',
default=None,
help='The name of the excel file containing CADET inputs.')
parser.add_argument('--expt-id',
default=None,
help='The name of the experiment to simulate.')
parser.add_argument('--skip-cadet',
action='store_true',
help=('Skip running CADET analysis if the file '
'already exisits.'))
parser.add_argument('--skip-plot',
action='store_true',
help=('Skip plotting the chromatograms.'))
parser.add_argument(
'--skip-anim',
action='store_true',
help=('Skip animations for each component concentrations.'))
parser.add_argument('-o',
'--output',
default=None,
help='The name of CADET simulation file.')
args = parser.parse_args()
if not isabs(args.log_dir):
log_dir = join(args.output_dir, args.log_dir)
else:
log_dir = args.log_dir
initialize_logging('run-chrom-sim',
verbose=args.verbose,
log_file=args.log,
log_dir=log_dir)
t0 = time.time()
run_chromatography_simulation(args.input_file,
args.output,
expt_id=args.expt_id,
skip_cadet=args.skip_cadet,
skip_plot=args.skip_plot,
skip_animation=args.skip_anim)
elapsed_time = time.time() - t0
msg = 'Elapsed time : {:0.2f} seconds'.format(elapsed_time)
logger.info(msg)
print(msg)
def _setup_logging(self):
from kromatography.utils.app_utils import get_preferences, \
initialize_logging
if self.verbose:
verbose = True
else:
preferences = get_preferences()
verbose = preferences.app_preferences.console_logging_level <= 10
self.log_filepath = initialize_logging(verbose=verbose)
for sim in sims:
output_file = prepare_simulation_for_run(sim)
yield run_cadet_simulator, (output_file,), {"use_slurm": use_slurm}
if __name__ == "__main__":
from traits.api import Any, Button
from traitsui.api import View, Item
from kromatography.model.tests.sample_data_factories import \
make_sample_simulation, make_sample_simulation_group2
from kromatography.utils.app_utils import initialize_logging
from kromatography.model.factories.job_manager import \
create_start_job_manager
initialize_logging(verbose=True)
sim = make_sample_simulation(name='Run_1')
NUM_JOBS = 1
NUM_WORK_ITEMS_PER_JOB = 2
NUM_SIM = NUM_JOBS * NUM_WORK_ITEMS_PER_JOB
t0 = time()
# runner1 = sim.run()
# group = make_sample_simulation_group2(size=2)
# runner2 = group.run(wait=True)
class SimpleGroupUI(HasStrictTraits):
group = Any
job_manager = Any
button = Button("Run sims")
def setUp(self):
self.log_file = abspath(join(HERE, "temp.log"))
initialize_logging(log_file=self.log_file)
def test_setuplogging_default_has_file(self):
initialize_logging()
self.assert_log_file_found()