Configuration files for optimization and simulation settings

ICB-DCM / pyPESTO

python Parameter EStimation TOolbox

https://pypesto.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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Configuration files for optimization and simulation settings #117

Open yannikschaelte opened 5 years ago

yannikschaelte commented 5 years ago

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 commented 5 years ago

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

yannikschaelte commented 5 years ago

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 commented 4 years ago

This is only loosely related to PEtab. Renaming.

dweindl commented 4 years ago

@yannikschaelte Any progress or concrete plans here?

yannikschaelte commented 4 years ago

No, unfortunately not, except for this slightly outdated branch https://github.com/ICB-DCM/pyPESTO/tree/feature_config_file