Use petablinter in example notebooks to demonstrate that the output is valid PEtab

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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Use petablinter in example notebooks to demonstrate that the output is valid PEtab #106

Closed yannikschaelte closed 3 years ago

yannikschaelte commented 3 years ago

Inserting a cell !petablint -v -y $petab_yaml_file (currently does not have a real python API).

jvanhoefer commented 3 years ago

actually, inside of of the validate_petab_tables function, the PEtab linter does exactly this

https://github.com/yaml2sbml-dev/yaml2sbml/blob/a8abacbb3a66eac4d92ed615a365c79e7aa56431/yaml2sbml/yaml2PEtab.py#L259

And this function again is called after every yaml2petab call...

Doesn't this resolve the problem? :)

jvanhoefer commented 3 years ago

here it is called inside yaml2petab https://github.com/yaml2sbml-dev/yaml2sbml/blob/a8abacbb3a66eac4d92ed615a365c79e7aa56431/yaml2sbml/yaml2PEtab.py#L114

Hence the user is informed, if the linter complains about the resulting PEtab problem

yannikschaelte commented 3 years ago

That's good! I was just wondering whether one wants to also explicitly have it in the notebooks to show to the user that all works, as the user may not know that all functions were internally already called.