Fast BOF

[jgilis]

One aspect hampering the use of Medusa for certain applications is the need to construct a list of GEMs prior to creating and analyzing the ensemble. Indeed, in many situations, it is computationally less expensive to create and analyze each member of the fly. This feature allows for directly populating the ensemble without needing to first generate each individual member, for one specific situation. This feature allows for directly populating an ensemble where members only differ w.r.t. their biomass objective function (BOF) definition. Note that as BOF coefficients can be set to zero, metabolites can either be omitted or admitted to the BOF. Changes made:

• bofEnsemble.py: workhorse
• test_boundsEnsemble.py: test validity
• TODO: Note that this branch also includes changes made in the maintenance, refactor_populate_features_base, and testBounds branches, I can undo this if this is inconvenient

Happy to discuss if functions like these would be a good fit for Medusa, or if they should be ported elsewhere.