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Fix compartment removal in reaction rates for sbml2bngl#421

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akutuva21 merged 1 commit into
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fix-sbml2bngl-compartment-removal-12651291564637042192
Jun 2, 2026
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Fix compartment removal in reaction rates for sbml2bngl#421
akutuva21 merged 1 commit into
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fix-sbml2bngl-compartment-removal-12651291564637042192

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Corrected a bug in SBML2BNGL.analyzeReactionRate where compartment sizes were incorrectly removed from reaction rate equations. The original code attempted to parse the numerator and denominator using as_numer_denom(), which failed on multi-term mathematical expressions (e.g., reversible reactions with minus signs) because subtraction prevents the extraction of a clean multiplicative denominator.

By substituting the compartment symbol with 1 using sym.subs(comp, 1), we cleanly remove its multiplicative effect regardless of where it appears in the mathematical expression. This robust symbolic approach accurately unrolls compartment size scaling from the rate laws.


PR created automatically by Jules for task 12651291564637042192 started by @akutuva21

Corrected a bug in SBML2BNGL.analyzeReactionRate where compartment sizes
were incorrectly removed from reaction rate equations. The original code
attempted to parse the numerator and denominator using `as_numer_denom()`,
which failed on multi-term mathematical expressions (e.g., reversible
reactions with minus signs). By substituting the compartment symbol with
`1` using `sym.subs(comp, 1)`, we cleanly remove its multiplicative effect
regardless of where it appears in the mathematical expression.

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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@akutuva21 akutuva21 marked this pull request as ready for review June 2, 2026 14:53
@akutuva21 akutuva21 merged commit 6612d48 into main Jun 2, 2026
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@akutuva21 akutuva21 deleted the fix-sbml2bngl-compartment-removal-12651291564637042192 branch June 2, 2026 14:53
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