Create_Ey_matrix only includes medium metabolites and not the bioproduct by default

[djinnome]

The external elasticity matrix ($E_y$) by default only includes metabolites in the medium. But we know that some metabolites that are produced should also belong in the elasticity matrix. Thus, should produced metabolites also appear in the $E_y$ matrix so that measurements of produced metabolites are included in the posterior distribution of $E_y$, or is the $E_y$ matrix exclusively for metabolites we can perturb (in which case, it should only be medium metabolites). In that case, external products would be part of the internal elasticity ($E_x$) matrix

emll/src/emll/util.py

Line 54 in a799ef2

boundary_indexes = [model.reactions.index(r) for r in model.medium.keys()]