RuleWorld / bionetgen

Rule-based modeling framework
https://bionetgen.org/
MIT License
56 stars 25 forks source link

Clean fix to catch species that refer to observables or functions #269

Closed ASinanSaglam closed 12 months ago

ASinanSaglam commented 12 months ago

A simple fix that uses existing functionality that errors out when BNG2.pl reads a species expression that refers to observables or functions. This is done because while the resulting .net file and model is accurate, this won't work with run_network or other downstream tools.

Now merging immediately until some discussion on whether we should fully error out or turn this into a warning.