Configuration files for optimization and simulation settings

[yannikschaelte]

For a start, introduce a configuration file (ini format?) that is not mandatory to the PeTab format, but which the petabimporter can read in and translate to amici and pypesto options.

The specifics and language of such a file can be revised later. Criteria: Human-readable, easy to edit, and easy to read in from different languages (mainly python, R, matlab).

This is needed in particular for serializing the model creation.

[dweindl]

I vote for YAML and could also live with less readable JSON. I think specifying lists and dictionaries in .ini is no fun.

[yannikschaelte]

agreed, ini is just for simple one-value options. yaml looks nice. python integration not that good apparently, but should be no problem using pyYAML.

what would be a possible use case for needing a list or dict? possibly the OptimizerOptions? these could be realized in ini also using sections.

[dweindl]

This is only loosely related to PEtab. Renaming.

[dweindl]

@yannikschaelte Any progress or concrete plans here?

[yannikschaelte]

No, unfortunately not, except for this slightly outdated branch https://github.com/ICB-DCM/pyPESTO/tree/feature_config_file