Non-linear solver not compatible with python versions >= 3.8

[azournas]

I am getting an error when running the file tutorial_synechocystis_inst_simulation.py, attached in this message. The jist of the problem is that openopt calls time.clock(), which is deprecated in python 3.3 and removed in python 3.8. As python 3.7 is not available in apple silicon, I can't think of an easy workaround.

For simulation purposes, since the fitter is not used, commenting out lines 23 and 24 from model.py, where the imports are happening, solves the problem, but it's not possible to run the estimation.

Is there a way to solve this issue with the existing code?

Thank you!

( freeflux % /Users/user/anaconda3/envs/freeflux/bin/python /Users/user/freeflux/tutorials/tutorial_synechocystis_inst_simulation.py
Traceback (most recent call last):
File "/Users/user/freeflux/tutorials/tutorial_synechocystis_inst_simulation.py", line 7, in
from freeflux import Model
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/freeflux/init.py", line 7, in
from .core.model import Model
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/freeflux/core/model.py", line 23, in
from ..analysis.fit import Fitter
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/freeflux/analysis/fit.py", line 20, in
from ..solver.nlpsolver import MFAModel
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/freeflux/solver/nlpsolver.py", line 13, in
from openopt import NLP
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/openopt/init.py", line 10, in
from oo import *
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/openopt/oo.py", line 4, in
from LP import LP as CLP
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/openopt/kernel/LP.py", line 1, in
from baseProblem import MatrixProblem
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/openopt/kernel/baseProblem.py", line 10, in
from ooIter import ooIter
File "/Users/user/anaconda3/envs/freeflux/lib/python3.9/site-packages/openopt/kernel/ooIter.py", line 3, in
from time import time, clock
ImportError: cannot import name 'clock' from 'time' (unknown location)

[Chaowu88]

Hi azournas, please refer to https://freeflux.readthedocs.io/en/latest/installation.html#dependencies-and-compatibility. You can use the corrected files to replace those in the openopt installation path.