Error assigning the bounds in _add_cycle_free

Is there an existing issue for this?

[X] I have searched the existing issues

Problem description

In the CycleFreeFlux paper, the bounds of each reaction are forced to be 0, and the initial optimization result.

However, in the _add_cycle_free implementation, when the original flux is > 0, the ub is forced to be the maximum value between the flux and the reaction ub, so this will always be the reaction ub. The same happens with the lb when the original flux is negative.

        if flux >= 0:
            rxn.bounds = max(0, rxn.lower_bound), max(flux, rxn.upper_bound)
            objective_vars.append(rxn.forward_variable)
        else:
            rxn.bounds = min(flux, rxn.lower_bound), min(0, rxn.upper_bound)
            objective_vars.append(rxn.reverse_variable)

Is there any reason for this way of assigning the bounds or is this a bug?

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 | 0.18.3 | | httpx | 0.25.1 | | importlib-resources | 6.1.1 | | isort | **missing** | | numpy | 1.26.1 | | optlang | 1.8.1 | | pandas | 2.1.2 | | pydantic | 2.4.2 | | python-libsbml | 5.20.2 | | rich | 13.6.0 | | ruamel.yaml | 0.18.5 | | scipy | 1.11.3 | | swiglpk | 5.0.8 | | tox | **missing** | ### Build Tools Information | Package | Version | |:-----------|--------:| | pip | 23.3.1 | | setuptools | 68.2.2 | | wheel | 0.41.3 | ### Platform Information | | | |:--------|------------------------------------:| | Linux | 4.18.0-477.15.1.el8_8.x86_64-x86_64 | | CPython | 3.10.13 |

opencobra / cobrapy