[BUG] Difficulties setting up Gurobi within COBRApy

[ivanmm25]

Is there an existing issue for this?

• I have searched the existing issues

Problem description

Hi! I was trying to set up the Gurobi solver within COBRApy, within a Python application container.

I followed the installation instructions for Gurobi in a Python-based docker container, either with a Gurobi-based image or with a Python-based image and simply installing gurobipy during build (this is working).

I requested a free academic WLS license and made it available within the container according to the indicated specifications. Finally, I tested the license with a couple of optimization examples (not involving COBRApy) and it was working.

However, when I was trying to execute COBRApy with the gurobi solver, I got an error while reading a VALID (XML format) model with cobra.io.read_sbml_model. This error is

CobraSBMLError: Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at https://sbml.org/validator_servlet/ . 	(model, errors) = validate_sbml_model(filename)` If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues. 

When executing (model, errors) = cobra.io.validate_sbml_model(modelpath), other than warnings there is a ‘COBRA_FATAL’ entry indicating ['addConstr() takes at most 3 positional arguments (4 given)'], which is unfamiliar to me.

Regarding my system, I am using python:3.12-slim as base image for the container, creating and executing a Python environment (version 3.12 again) within the container and installing libraries (cobra==0.29.0, gurobipy==12.0.0) within this environment.

Note that available solvers are displayed when I execute cobra.core.configuration.SOLVERS ('gurobi': <module 'optlang.gurobi_interface' from '/opt/intvenv/lib/python3.12/site-packages/optlang/gurobi_interface.py'>), and that a connection is established (a token is created) when my code tries to access my Gurobi WLS license.

Set parameter WLSAccessID  
Set parameter WLSSecret  
Set parameter LicenseID to value ... 
[client] info : [...] 
[client] info : Validate token ... 
[client] info : *** Academic license ... - for non-commercial use only - registered to [email address]  
[client] info: Token is valid 

Could you please help me? Also do not hesitate to ask for additional information in case I forgot to provide it. Thank you very much!

Environment

### Package Information

Package	Version
cobra	0.29.0

Dependency Information

Package	Version
appdirs	1.4.4
black	missing
bumpversion	missing
depinfo	2.2.0
diskcache	5.6.3
future	1.0.0
httpx	0.28.1
importlib-resources	6.4.5
isort	missing
numpy	2.1.1
optlang	1.8.2
pandas	2.2.2
pydantic	2.10.3
python-libsbml	5.20.4
rich	13.9.4
ruamel.yaml	0.18.6
scipy	1.14.1
swiglpk	5.0.12
tox	missing

Build Tools Information

Package	Version
pip	24.3.1
setuptools	75.6.0

Platform Information

Linux	6.8.0-49-generic-x86_64
CPython	3.12.8

[cambordas]

This problem originates from optlang opencobra/optlang#273 . I managed to overcome this for the time being using gurobipy version 11.0.3

[ivanmm25]

Okay, thank you very much! By any chance, do you know if we can expect the bug to be fixed to update gurobipy to the latest version at some point?

[cdiener]

As @cambordas said this was due to an incompatibility in optlang. It is already fixed there and will be part of the next release. Downgrading gurobi will work for now.

[ivanmm25]

All clear, thank you, @cdiener!