Design CLI Options

[kwabenantim]

Summary

chaste-codegen-sbml [--model-type=MODELTYPE] [--timescale=TIMESCALE] [--output-dir=PATH] SBML_FILE

--model-type=MODELTYPE
    Possible options: generic | srn | cell-cycle

--timescale=TIMESCALE
   Possible options: ms | s | m | h 

To Do

• Allow user to specify model type:
  • SRN model
  • Cell Cycle model
  • Generic model with an ODE system
• Allow manually specifying model timescale (flag if we can't find automatically to let user set -- warn if setting differs from model)
• Allow solver selection e.g. RungeKutta4IvpOdeSolver or CVODE. See comment.: Use sensible default instead. Solver can be set before model run.
• Allow setting solver SetDt(0.1) : Use sensible default instead. Value can be changed before model run.

[kwabenantim]

Currently, chaste-codegen-sbml assumes that a model is a Cell Cycle model if it contains events and an SRN model if it has no events. This assumption will be removed and made a command line option, defaulting to SRN.

Update

The default is to create just an OdeSystem. If srn is specified in the command line, a corresponding SrnModel will be created as well. If cell-cycle is specified instead, a corresponding CellCycleModel will be created instead.