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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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Refactor SBML sympification #2146

Open dweindl opened 1 year ago

dweindl commented 1 year ago

At some point it would be convenient to replace the current SBML-sympification by https://github.com/dweindl/sbmlmath/. This gives us better control over the whole process and can replace the awkward log and piecewise handling, handling of SBML constants and special functions. And the initial collection of all SBML symbols would become obsolete. Not expecting a relevant speed gain, but improved maintainability.

dweindl commented 4 months ago

Furthermore, I think the current sympification is problematic because of differences in operator precedence between SBML L3 formula strings and sympy (which is based on Python rules) that are ignored in amici.