Fix SBML math parsing - #509
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sympy.sympify(formulaToL3String(...)) applies Python operator semantics to SBML L3 formulas, which silently diverge for constructs like modulo (sign-of-dividend in SBML vs. sign-of-divisor in Python). Parse the SBML MathML directly via sbmlmath instead. Fixes PEtab-dev#283
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #509 +/- ##
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+ Coverage 75.57% 75.61% +0.04%
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Files 65 65
Lines 7357 7354 -3
Branches 1323 1323
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+ Hits 5560 5561 +1
+ Misses 1293 1289 -4
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dweindl
marked this pull request as ready for review
August 12, 2026 08:13
dilpath
approved these changes
Aug 12, 2026
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| def test_sympify_sbml_modulo(): | ||
| """SBML's ``%`` follows C semantics (result has the sign of the | ||
| dividend), unlike Python's ``%`` (result has the sign of the divisor). | ||
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| Naively converting the SBML math to a string and handing it to | ||
| ``sympy.sympify`` therefore silently produces a wrong result (gh-283). | ||
| """ | ||
| sbml_document = libsbml.SBMLDocument(3, 2) | ||
| sbml_model = sbml_document.createModel() | ||
| parameter = sbml_model.createParameter() | ||
| parameter.setId("e") | ||
| parameter.setConstant(False) | ||
| initial_assignment = sbml_model.createInitialAssignment() | ||
| initial_assignment.setSymbol("e") | ||
| initial_assignment.setMath(libsbml.parseL3Formula("-5 % 3")) | ||
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| assert sympify_sbml(initial_assignment).doit() == -2 |
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It can be added there as well, but I think it makes sense to have it here. This tests exactly what changed in this PR. Would have failed before, passes now.
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sympify_sbmlnow parses SBML MathML directly viasbmlmath.sbml_math_to_sympyinstead of round-tripping throughlibsbml.formulaToL3String+sympy.sympify, which silently applies Python operator semantics to SBML L3 formulas.sbmlmathfrom thedocextra to a core dependency, sincepetab.v1now needs it unconditionally.%uses sign-of-dividend semantics, Python's%uses sign-of-divisor — the old code silently returned the wrong value for negative operands.Fixes #283