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Adds the new command primarypairs for predicting reactant/product element transfers using the new FindPrimaryPairs method as well as the MapMaker method.
A new option has been added to the genedelete command which allows use of minimization of metabolic adjustments to simulate biomass production for gene knockouts.
Fixes a bug where the epsilon parameter was accidentally ignored by fastgapfill.
Fixes a bug where the psamm-sbml-model command did not ignore boundary species. With this change, the boundary species are also ignored by default when using the API to read SBML models.
Fixes a performance issues with gap-filling that made the gapfill and fastgapfill commands take much longer time to run on large models than necessary.