chaowu88 / freeflux Goto Github PK

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)

I just installed freeflux and it works well with Python 3.10. Thank you for such an important contribution. I am wondering if freeflux can solve fluxes by combining data from different tracer experiments? For example, I have MDV measured in two experiments, one using 1,2-C13 glucose and the other using 1,6-C13 glucose. Can data from both experiments analyzed together? Thank you!

Hi, thanks for putting together this package, great job! We have been trying it out in our lab and it looks promising so far.

However, I ran a problem when using the InstFitter class to fit time-series data -- I noticed that calling InstFitter.prepare erases any concentration bounds in InstFitter.model.concentrations_bounds, such as bounds previously set with InstFitter.set_concentration_bounds. I found that prepare calls _set_default_concentration_bounds which seems to have a bug at this line:

Apparently it's checking model.net_fluxes_bounds instead of concentrations_bounds.

I can submit PR with a bug fix if helpful, let me know. Thanks!