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

Export expressions as SBML assignment rules #372

merged 5 commits into from Oct 16, 2018


None yet
3 participants

FFroehlich commented Sep 4, 2018

Rationale behind this change is that assignment rules, compared to functions, are easier to access/evaluate programmatically.


This comment has been minimized.

coveralls commented Sep 4, 2018

Coverage Status

Coverage increased (+0.6%) to 79.053% when pulling 477b1dc on FFroehlich:master into 4993362 on pysb:master.

export sbml reaction names according to the rules they implement and …
…dont expand the expression in exported sbml InitialAssignment

Looks good. BioNetGen also uses assignment rules when it exports SBML, so there's precedent for this approach.

The new naming convention for reactions means they're no longer guaranteed to be unique, but that shouldn't be an issue since the ID can be used to disambiguate.

@alubbock alubbock merged commit c99fe27 into pysb:master Oct 16, 2018

2 checks passed

continuous-integration/appveyor/pr AppVeyor build succeeded
continuous-integration/travis-ci/pr The Travis CI build passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment