[BUG] COBRApy overwriting label content #25
Description
Currently, when a model is loaded and subsequently written with COBRApy before and after working on it with libSBML, its labels get overwritten.
Since the gap-filling with the GeneGapFiller in the HQTB workflows relies on these labels for identification, running it twice (in extension and cleanup) leads to problems.
As a quick fix, the polish function of refineGEMs is called in-between in an attempt to restore the labels but time and potentially information is lost.
Ideally, the labels should be added directly to the COBRApy model (see issue there).
Currently, there is no fast or easy solution from inside SPECIMEN for this.