integrate RIPTiDe into DEXOM
RIPTiDe references:
https://pmc.ncbi.nlm.nih.gov/articles/PMC7188308/
https://github.com/mjenior/riptide/tree/master
https://pypi.org/project/riptide/
TODO:
In all enumeration functions:
- add a parameter allowing to choose between imat & riptide
- add an if-else to switch between the two
In rxn-enum & icut:
- replace calls to imat with calls to riptide.contextualize
- extract fluxes & binaries from solution object
In maxdist and diversity-enum:
- replace create_maxdis_constraint with create_riptide_constraint
- need 2 constraints: minimize pruning coefficients, maximize sampling coefficients (see github code lines 1024 & 1046, publication subsections "Linear coefficient assignment" and "Flux sampling")
Edited by Maximilian Stingl