What's Changed

• FVA correction in #12
• Fixed translocases flag issue, seen with the Synechocystis clean model.

Full Changelog: v1.2.1...v1.2.2

Ended support for python 3.7

What's Changed

• Implemented CLI coralme command in #8
• Refactoring simulation methods into optimization.py in #7
• Added Bacillus subtilis as a choosable reference in coralME in #9

Full Changelog: v1.1.12...v1.2.0

1. New unit system in place using pint
2. Corrected model.from_cobra method to set genes into all_genes, and related methods
3. Updated methods to account for units in stoichiometric coefficients, bounds, and reconstruction parameters
4. Updated DNA replication functions to consider a symbolic expression
5. Extended coralME M-models to consider cofactor information in reactions: New reaction.functional method based on cobrapy's reaction.functional, and modified model.construct_lp_problem to determine not functional reactions
6. Updated util.model2excel and util.excel2model functions to save and read M-models with cofactor data in reactions
7. Updated save and read JSON files, to correct the lack of values from v1.0 files
8. New feasibility limit and minor style changes such as int to floats
9. Fixed deprecated methods, such as Biopython's SeqFeature.strand and cobrapy's gene.parse_string

1. optimize with get_reduced_costs=True now works with new per_position setting of construct_lp_problem. It was not setting per_position=True, causing an error
2. Allow calling other solvers using model.optimize(solver=solver)
3. Corrected annotation of solver functions
4. Extended solver flag across troubleshooting. Should not import qwarmLP when using gurobi instead of qminos
5. Fixed overall compatibility with MacOS. MacOS can run without qminos installed and only with gurobi.

1. Tested compatibility with python 3.7

1. Update README.rst
2. More elegant handling of python 3.7 compatibility
3. Fixed compatibility with python3.7, sympy.lambdify(list(atoms), lb, docstring_limit = None)
4. Allow MacOS users to import coralme.solver
5. Allowed the definition of RNAP in configuration
6. Added info to docs

1. Save to JSON new 'pseudo' property in processdata
2. JSON stores translation table as string
3. Fixed compatibility with gurobi and cplex
4. Corrected savefile default and user input values
5. Set default solver as qminos

1. New essentiality.py module to perform gene knockouts and metabolite supplementation
2. New model methods: MEModel.from_cobra, MEModel.minimize, MEModel.copy
3. Code improvement: SyntaxWarnings and new logging messages
4. New reconstruction options: flux_of_dna_constituents and genetic_recoding
5. New HTML representation for models: Shows total number of process_data and pseudogenes in the reconstruction
6. New HTML representation for reactions: Shows if the reaction is mass balanced
7. New shortcuts in model: MEModel.perform_gene_knockouts, MEModel.to_json, and MEModel.to_pickle
8. New shortcuts in components: MEComponent.add_boundary and MEComponent.get_fluxes
9. Corrected MEReaction.copy and added ProcessData.copy
10. Now you can choose solver for troubleshooting the model, e.g. solver="gurobi"

1. Removed print in get_graph function
2. GPR combination cutoff works, solved bug, stable version. This allows to stop the combinatorial explosion before it happens, necessary for >10k combinations from long GPRs in some models. Before: coralME would take several minutes computing all combinations and then not using them due to the length of the list. Now: coralME identifies it crossed the cutoff (default = 100) and stops.