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opensir-cli
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opensir-cli
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#!/usr/bin/env python3
# pylint: disable=C0103
""" Open-SIR CLI implementation """
import argparse
import sys
import toml
from opensir.models import SIR, SIRX
MODEL_SIR = 0
MODEL_SIRX = 1
def run_cli():
""" This function runs the main CLI routine """
parser = argparse.ArgumentParser(description="""
Run SIR or SIR-X model given a set of initial conditions and model
parameters.
""")
parser.add_argument("-m", "--model", default="sir", choices=["sir", "sirx"])
parser.add_argument("-t", "--time", type=int, help="Number of days for "
"the simulation")
parser.add_argument("-f", "--file", type=str, help="Name of the "
"input file. If missing, the input file is read from STDIN")
parser.add_argument("-s", "--suppress_header", action="store_true",
help="Suppress CSV header")
parser.add_argument("-d", "--delimiter", type=str, help="CSV delimiter",
default=",")
args = parser.parse_args()
if args.file is None:
data = toml.loads(sys.stdin.read())
else:
data = toml.load(args.file)
ic = data["initial_conds"]
params = data["parameters"]
model = MODEL_SIR if args.model == "sir" else MODEL_SIRX
kwargs = {}
if args.time:
kwargs["tf_days"] = args.time
if model == MODEL_SIR:
p = [params["alpha"], params["beta"]]
w0 = [ic["S0"], ic["I0"], ic["R0"]]
sol = SIR()
else:
p = [params["alpha"], params["beta"], params["kappa_0"],
params["kappa"]]
w0 = [ic["S0"], ic["I0"], ic["R0"], ic["X0"]]
sol = SIRX()
sol.set_params(p, w0).solve(**kwargs).export(sys.stdout,
suppress_header=args.suppress_header,
delimiter=args.delimiter)
if __name__ == "__main__":
run_cli()