Relaxation of log concentration error about pytfa

[psalvy]

Good day Svetlana,

The second error is infeasibility with the Gurobi solver, mishandled by cobra. Probably the lower bound you ask for is higher than the achievable objective function in the TFA problem. Since this happens at the beginning of the relax_lc function, this suggests that your TFA model cannot achieve that high a growth rate.

The first error looks like it wants to relax 0 constraints, so the table has 0 elements and no columns, and the column name change is crashing because of that. That is because with a lower bound of 0, there is by definition no relaxation to be made.

These two items (infeasible model at the beginning of the function + no relaxation needed) seem to suggest the TFA model grows much slower than FBA predictions.

Could you try:

1. Optimize the tfa model with no relaxation nor extra constraints. Report the solution value
2. Ask for relaxation with a very low non-zero lower bound (1e-3 for example). What is the result ?
3. When you get infeasibility, run the function debug_iis from the debugging module. This will give you a list of infeasible constraints / variable bounds. If there is around or less than 10 of each, can you post them here please ?
4. Also, are you using DeltaG from eQuilibrator or from the provided `thermo_data' ? how much of your model is covered by thermodynamics ?

Cheers,
Pierre