Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

omit conversion to mass action for stoichiometries > 100 to avoid StackOverflow in simplify_fractions #161

Merged
merged 6 commits into from
Jul 4, 2024

Conversation

paulflang
Copy link
Member

Checklist

  • [ x] Appropriate tests were added
  • [x ] Any code changes were done in a way that does not break public API
  • [x ] All documentation related to code changes were updated
  • [x ] The new code follows the
    contributor guidelines, in particular the SciML Style Guide and
    COLPRAC.
  • [x ] Any new documentation only uses public API

Additional context

This is to fix #160 . The model in question contains stoichiometries in excess to 1e4, which causes StackOverflow in SymbolicUtils.simplify fractions. The fix here is to no longer attempt to recover mass action kinetics from generic SBML rate laws whenever reactant stoichiometry is >100. This circumvents the need for calling simplify_fractions.

@paulflang paulflang marked this pull request as ready for review July 4, 2024 01:03
@paulflang paulflang merged commit 18ebab7 into main Jul 4, 2024
6 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Error constructing reaction system from SBML BioModel
1 participant