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yaml2sbml-dev / yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.
https://yaml2sbml.readthedocs.io/en/latest/
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Definition of Model ID for use with pyPESTO and AMICI #101

Closed elbaraim closed 3 years ago

elbaraim commented 3 years ago

Currently when a new model is created after using this wonderful tool the model field read as <model>

This leads (when used together with pyPESTO and AMICI) to the generation of a random name which is used as name for the model in the amici folder, e.g. amici_models/tmpiouv7fa5. The problem here is that every time one will load the model, the random name is changing, therefore the already compiled folder is not detected, and the model is compiled again.

This has a very simple fix. During the model creation you can add the model ID, such that the final sbml model will contain <model id="MyModelName" name="MyModelName"> instead of <model>

I do not know how this behaves for other tools, but for pyPESTO/AMICI this would be a valuable fix.

yannikschaelte commented 3 years ago

I agree that filling the model id consistently into the various places it's used (in the sbml, as folder names etc) is a good idea. Currently, the model has no id, so this should be easy to fix.

jvanhoefer commented 3 years ago

similarly it would be great, if the model name is somehow reflected in the created PEtab tables of yaml2petab. So let's go for

observables_<model_name>.tsv instead of observable_table.tsv as currently...

jvanhoefer commented 3 years ago

So, all of that is done, only this breaks the tests, that compare the result of SBML conversion to a precomputed SBML...