Template for Model Run

import datetime
import logging
import os
from pathlib import Path

from tlo import Date, Simulation
from tlo.analysis.utils import parse_log_file
from tlo.methods import (
    chronicsyndrome,
    contraception,
    demography,
    dx_algorithm_child,
    enhanced_lifestyle,
    healthburden,
    healthseekingbehaviour,
    healthsystem,
    mockitis,
    symptommanager,
)

# Output path [NB. Working directory must be set to the root of TLO: TLOmodel]
outputpath = Path('./outputs')

# The Resource files [NB. Working directory must be set to the root of TLO: TLOmodel]
resourcefilepath = Path('./resources')

# Establish the simulation object
start_date = Date(year=2010, month=1, day=1)
end_date = Date(year=2010, month=12, day=31)
popsize = 2000
sim = Simulation(start_date=start_date)

# date-stamp to label log files and any other outputs
datestamp = datetime.date.today().strftime("__%Y_%m_%d")

# Establish the logger``
logfile = outputpath + 'LogFile' + datestamp + '.log'

if os.path.exists(logfile):
    os.remove(logfile)
fh = logging.FileHandler(logfile)
fr = logging.Formatter("%(levelname)s|%(name)s|%(message)s")
fh.setFormatter(fr)
logging.getLogger().addHandler(fh)

# Make all services available:
service_availability = ['*']

# Register the appropriate modules``
sim.register(demography.Demography(resourcefilepath=resourcefilepath))
sim.register(contraception.Contraception(resourcefilepath=resourcefilepath))
sim.register(enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath))
sim.register(healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
                                       service_availability=service_availability,
                                       mode_appt_constraints=2,
                                       capabilities_coefficient=1.0,
                                       ignore_cons_constraints=False,
                                       disable=False))
# (NB. will run much faster with disable=True in the declaration of the HealthSystem)
sim.register(symptommanager.SymptomManager(resourcefilepath=resourcefilepath))
sim.register(healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath))
sim.register(dx_algorithm_child.DxAlgorithmChild(resourcefilepath=resourcefilepath))
sim.register(healthburden.HealthBurden(resourcefilepath=resourcefilepath))


# Register disease modules:
# << ---- >>

# Run the simulation and flush the logger
sim.seed_rngs(0)
sim.make_initial_population(n=popsize)
sim.simulate(end_date=end_date)
fh.flush()

# Read the results
output = parse_log_file(logfile)