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Export expressions as SBML assignment rules #372

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merged 5 commits into from Oct 16, 2018

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@FFroehlich
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FFroehlich commented Sep 4, 2018

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

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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
@alubbock

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

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