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

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.