[Feature request]: configuration file specification of initial conditions

[pearsonca]

Label

enhancement, gempyor

Priority Label

high priority

Is your feature request related to a problem? Please describe.

Need to refactor initial conditions such that configuration file specification for initial conditions works the same way as parameters.

Is your feature request related to a new application, scenario round, pathogen? Please describe.

No response

Describe the solution you'd like

This refactoring should:

• internally: do nothing different with how initial conditions are used (obviously will need to change how they are parsed out). this is just update to how initial conditions are specified in config
• prefer: deprecate the current approach to initial conditions. warn the user about deprecation, and emit the rewritten yaml they can substitute.
• alt: break the current approach. provide a tool for translating initial conditions into the new format?
• alt: provide no support & force user updates

Currently, the example initial conditions look like:

initial_conditions:
  method: SetInitialConditions
  initial_conditions_file: model_input/ic_2pop.csv
  allow_missing_subpops: TRUE
  allow_missing_compartments: TRUE

and

initial_conditions:
  method: plugin
  plugin_file_path: model_input/my_initial_conditions.py

This should become something like:

...
parameters:
  X0:
    type: file
    value: model_input/ic_2pop.csv
    allow_missing_subpops: TRUE
    allow_missing_compartments: TRUE
...

where for now we have a special variable name for initial conditions (X0), which would later lose its special status, but likely stick around as a naming convention. type will distinguish between e.g. a file, a plugin to run, as well as a prior, a fixed value, etc, etc.