PERFORMANCE: create_smoment_model_reaction_wise_with_sbml gets bogged down in recent cobrapy release

[yaccos]

This is an issue I think is due to updates in cobra. With cobra version 0.21.0 create_smoment_model_reaction_wise_with_sbml() runs in a reasonable amount of time. However, once I use an environment with cobra version 0.26.3, the same function consumed a prohibiting amount of time. After drilling into the details, I realized that the time was spent deepcopying metabolic reactions

autopacmen/autopacmen/submodules/helper_create_model.py

Line 186 in e115b91

forward_reaction = copy.deepcopy(reaction)

From my understanding, the autoPACMEN code has not changed on this point, but cobra probably has changed its procedures for copying reactions, leading to a very slow recursive process. As a side note, I have experienced cobrapy to be slow and cumbersome for modifying models and their components. There exist an alternative metabolic modeling package named reframed which I have used to resolve such problems, but due to technological dept, replacing cobra with reframed would take a considerable effort.

[mretier]

I had the same problem, thanks for pointing this out. It helped me resolve the issue.