Cobamp

Added
- Constraint-based simulator class that facilitates batch simulations on the same model with
the possibility of changing environmental conditions and objective functions

Changed
- Wrappers module now automatically loads readers that can be used - this is done by attempting
to import each associated package.

Removed
- GIMME and CORSO model objects, now appropriately a part of the troppo framework

Added
- ConstraintBasedModel simplification based on FVA
- GPR evaluation class that detaches GPR evaluation from models and readers
- Genetic minimal cut sets
- Parameters to ignore GPRs that cannot be parsed due to computational demand
- Method to identify boundary reactions on ConstraintBasedModels
- EFM-based methods can now include a "non_produced" parameter for metabolites that are optionally consumed but
never produced
- With expressions can now be used on ConstraintBasedModels to allow context on reaction and metabolite changes

Changed
- Bugfixes on GPR evaluation and reading
- Singular add/remove methods for reactions/metabolites to be deprecated in the future

Added
- Benders decomposition solver (this is a very experimental feature)
- Multiprocessing utilities (mp_utils)
Changed
- Several bugfixes and additional features for LinearSystem classes

Changed
- Version revision

Added
- Memory and thread setting parameters on LinearSystem / algorithm classes

Changed
- Bugfixes concerning GPR reading (Gene names had an additional underscore character)
- Normalized LinearSystem class argument signature
- Linear systems with lower and upper bounds now properly check for irreversible reactions in the opposite direction