Missing extracellular compartment in exported models

[pwendering]

A related question (but we can migrate this to a new Issue if you prefer): your paper mentions adding transport reactions from cytosol to extracellular space when necessary. But the SBML models (whether from write_models_sbml.m or write_models_sbml_raw.m) only have one compartment, cytosol (though some of the metabolite names still have the "[e]" suffix). Do you know if the lack of an extracellular compartment is an exporting error, or was it necessary/intentional?

Originally posted by @zoey-rw in #2 (comment)

[pwendering]

Does this mean that you don't have any reactions with suffix "_e" after reading the SBML file?

When I imported the models using the COBRA toolbox for Matlab, all metabolites and reactions were still present (as well as fields .comps and .compNames). Could you please check if this problem only occurs with Python or also with Matlab?