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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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Make ODE specification optional #142

Open shoepfl opened 1 year ago

shoepfl commented 1 year ago

Hi,

at the moment the specification of an ODE is mandatory in yaml2sbml, this is problematic when one wants to use explicit equations.

As SBML also supports only the specification of explicit equations, see: https://github.com/sbmlteam/libsbml/issues/318

I would suggest to make the specification of an ODE optional like an assignment rule.

Thanks for your help

dilpath commented 1 year ago

Hi @shoepfl , sorry for the delay. I just made a PR for this. It looks as simple as editing the file "yaml2sbml/yaml_schema.yaml" and removing the last three lines [1]:

required:
  - odes

This works for me with the following simple example:

time:
      variable: t

assignments:
    - assignmentId: x_1
      formula: exp(t)

[1] https://github.com/yaml2sbml-dev/yaml2sbml/pull/143/files

shoepfl commented 1 year ago

Hi @dilpath,

ok thanks this looks good and also works for my example :)