Major changes between versions will be documented on this file.
- Constraint-based simulator class that facilitates batch simulations on the same model with the possibility of changing environmental conditions and objective functions
- Wrappers module now automatically loads readers that can be used - this is done by attempting to import each associated package.
- GIMME and CORSO model objects, now appropriately a part of the troppo framework
- 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
- Bugfixes on GPR evaluation and reading
- Singular add/remove methods for reactions/metabolites to be deprecated in the future
- Benders decomposition solver (this is a very experimental feature)
- Multiprocessing utilities (mp_utils)
- Several bugfixes and additional features for LinearSystem classes
- Version revision
- Memory and thread setting parameters on LinearSystem / algorithm classes
- 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
- Gene protein reaction rule evaluation module (cobamp.gpr.evaluators). Still a work in progress but the aim is to eventually move all GPR code into this module upon releasing a major revision
- New dependency (boolean.py)
- Fixed errors in the readthedocs quickstart example
- Corrected some assorted bugs on the ConstraintBasedModel and KShortest classes
- This should be the last release without CI/CD
- Several bug fixes
- KShortest algorithm now adds constraints iteratively to avoid memory errors
- Several improvements to the ConstraintBasedModel class
- Big-M indicators for solvers without a dedicated indicator constraint abstraction
- SCIPY MAT format model reader
- Gene-protein-rule support with gene expression data integration functions
- Analysis functions (mainly frequency and graphs) with some plotting capability
- Transformer classes for algorithms that alter a metabolic network, guaranteeing mapping between the reactions of both
- Higher-level classes (linear_systems module) for semi-efficient definition of LP problems based on Optlang
- Classes for evaluating and converting into postfix type arithmetic and boolean expressions
- Major code refactor. Module structure drastically changed and reorganized.
- Many bugfixes
- Basic metabolic model classes for when an SBML file is not available or necessary
- Elementary flux pattern enumeration using the K-Shortest algorithm (as a wrapper)
- Entire package structure to accomodate other types of algorithms beyond the K-Shortest one
- Some modules that were too specific for the changes above
- Base code for K-Shortest enumeration of EFMs and MCSs
- Core framework architecture (linear systems, algorithms and wrappers)
- COBRApy and framed model object readers