the method of cometspy.comets() can not working properly

[wupeng1998]

when i use cometspy to simulation, i find the method can not working properly. here is my test code: import cobra.test import cometspy as c from cometspy.utils import chemostat

make a model from a cobra model, open exchange reactions, and give a pop

tb = cobra.test.create_test_model("textbook")
m = c.model(tb)
m.initial_pop = [0, 0, 1.e-4]
m.open_exchanges()
reservoir = {'glc__D_e': 0.01, 'nh4_e': 1000., 'pi_e': 1000.}
c.layout, c.params = chemostat([m], reservoir, 0.1)
c.params.set_param("maxCycles", 100)
sim = c.comets(c.layout, c.params)
sim.run()
print(sim.total_biomass)

And there is the screenshot of my error.

[jeremymchacon]

Hello, that means that the COMETS_HOME environmental variable was not found. It should have been set during COMETS installation (which is separate from and necessary to use cometspy, and can be downloaded at runComets.org) .

If you do have COMETS installed and for some reason the variable is not present in your python env, you can set it at the top of your script with the os package:

import os os.environ['COMETS_HOME'] = '/home/jeremy/comets/'

where /home/jeremy/comets is where comets is on your system.