Fix SBML math parsing by using sbmlmath instead of sympy.sympify

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 #283

Author: dweindl

petab/v1/models/sbml_model.py

@@ -8,7 +8,7 @@
 
 import libsbml
 import sympy as sp
-from sympy.abc import _clash
+from sbmlmath import sbml_math_to_sympy
 
 from ..._utils import _generate_path
 from ..sbml import (
@@ -283,28 +283,7 @@ def sympify_sbml(sbml_obj: libsbml.ASTNode | libsbml.SBase) -> sp.Expr:
     -------
     The sympy expression corresponding to ``sbml_obj``.
     """
-    ast_node = (
-        sbml_obj
-        if isinstance(sbml_obj, libsbml.ASTNode)
-        else sbml_obj.getMath()
-    )
-
-    parser_settings = libsbml.L3ParserSettings(
-        ast_node.getParentSBMLObject().getModel(),
-        libsbml.L3P_PARSE_LOG_AS_LOG10,
-        libsbml.L3P_EXPAND_UNARY_MINUS,
-        libsbml.L3P_NO_UNITS,
-        libsbml.L3P_AVOGADRO_IS_CSYMBOL,
-        libsbml.L3P_COMPARE_BUILTINS_CASE_INSENSITIVE,
-        None,
-        libsbml.L3P_MODULO_IS_PIECEWISE,
-    )
-
-    formula_str = libsbml.formulaToL3StringWithSettings(
-        ast_node, parser_settings
-    )
-
-    return sp.sympify(formula_str, locals=_clash)
+    return sbml_math_to_sympy(sbml_obj)
 
 
 def antimony2sbml(ant_model: str | Path) -> str:

pyproject.toml

@@ -20,6 +20,7 @@ dependencies = [
     "jsonschema",
     "antlr4-python3-runtime==4.13.1",
     "pydantic>=2.10",
+    "sbmlmath>=0.4.0",
 ]
 license = "MIT"
 authors = [
@@ -64,7 +65,6 @@ doc = [
     "ipython>=7.21.0, !=8.7.0",
     "pysb",
     "antimony>=2.14.0",
-    "sbmlmath>=0.4.0",
 ]
 vis = [
     "matplotlib>=3.6.0",

tests/v1/test_sbml.py

@@ -5,7 +5,7 @@
 import pandas as pd
 import pytest
 
-from petab.v1.models.sbml_model import SbmlModel
+from petab.v1.models.sbml_model import SbmlModel, sympify_sbml
 
 sys.path.append(os.getcwd())
 import petab  # noqa: E402
@@ -150,3 +150,22 @@ def test_sbml_from_to_ant():
 
     # convert back to antimony
     assert "R1: S1 -> S2; k1*S1" in petab_model.to_antimony()
+
+
+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).
+
+    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"))
+
+    assert sympify_sbml(initial_assignment).doit() == -2