Issues with com.cooperative_tradeoff

[Rotembartuv]

Hi,

I'm trying to read my models and get an error...
this Is my code:
My medium is a dict; the pickel file holds 4 bacteria.

For com_No in all_com:
    com_name = 'com0' + str(com_No) + '.pickle'
    com = load_pickle('C:/Users/rotemb/OneDrive/Ph.D/communities/com_models/' +
                      com_name)
    com.medium = rSSM
    sol = com.cooperative_tradeoff(fraction=0.9)
    temp_sol = pd.DataFrame(sol.members)
    temp_sol.insert(0, "community number", ["sample_"+str(com_No), "sample_"+str(com_No),
                                            "sample_"+str(com_No), "sample_"+str(com_No), "sample_"+str(com_No)])
    temp_sol.insert(0, "compartments", temp_sol.index)
    all_com_sol = pd.concat([all_com_sol, temp_sol], axis=0)
    print(com_No)

The first file works:

all_com_sol
        compartments community number  abundance  growth_rate reactions  \
GSMM_43      GSMM_43         sample_1       0.33     0.321494      1893   
GSMM_46      GSMM_46         sample_1       0.33     0.164969      2623   
gsmm_47      gsmm_47         sample_1       0.33     0.280011      2321   
medium        medium         sample_1        NaN          NaN       405   
peni            peni         sample_1       0.01     0.005702      1837   

        metabolites  
GSMM_43        1308  
GSMM_46        1758  
gsmm_47        1587  
medium          405  
peni           1288  

But the second (and following files) fails...
The error I get is:

File "C:\Users\rotemb\AppData\Local\Temp/ipykernel_25904/3715535988.py", line 9, in <module>
    sol = com.cooperative_tradeoff(fraction=0.1)

  File "C:\Users\rotemb\Anaconda3\lib\site-packages\micom\community.py", line 797, in cooperative_tradeoff
    return cooperative_tradeoff(

  File "C:\Users\rotemb\Anaconda3\lib\site-packages\micom\problems.py", line 92, in cooperative_tradeoff
    com.variables.community_objective.ub = min_growth

  File "C:\Users\rotemb\Anaconda3\lib\site-packages\optlang\interface.py", line 227, in ub
    raise ValueError(

ValueError: The provided upper bound -6.34344e-05 is smaller than the lower bound -6.34344e-06 of variable -6.343436825865402e-06 <= community_objective <= inf.

What is the problem?
Thanks

[cdiener]

So sorry for the delay, I completely missed this question.

It looks like your models can't grow on the provided medium since the maximum growth rate is estimated as -6e-6 (that is close to zero within the solver tolerance)... What do you get when you run the following?

sol = com.optimize()
print(sol)
print(sol.members)