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fix #2642 #2643

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Feb 5, 2025
Merged

fix #2642 #2643

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a88c056
fix #2642
FFroehlich Jan 31, 2025
c0c0cdf
fixup
FFroehlich Jan 31, 2025
3ff2c9d
fixup
FFroehlich Jan 31, 2025
f72a694
add issue as regression test
FFroehlich Feb 5, 2025
a0e3113
fix path
FFroehlich Feb 5, 2025
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26 changes: 23 additions & 3 deletions python/sdist/amici/sbml_import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2292,9 +2292,29 @@

sym_math, rateof_to_dummy = _rateof_to_dummy(sym_math)

for species_id, species in self.symbols[SymbolId.SPECIES].items():
if "init" in species:
sym_math = smart_subs(sym_math, species_id, species["init"])
# we can't rely on anything else being properly initialized at this point, so we need to
# compute all initial values from scratch, recursively
for var in sym_math.free_symbols:
element_id = str(var)
# already recursive since _get_element_initial_assignment calls _make_initial
if (
ia := self._get_element_initial_assignment(element_id)
) is not None:
sym_math = sym_math.subs(var, ia)
elif (species := self.sbml.getSpecies(element_id)) is not None:
# recursive!
init = self._make_initial(get_species_initial(species))
sym_math = sym_math.subs(var, init)

Check warning on line 2307 in python/sdist/amici/sbml_import.py

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python/sdist/amici/sbml_import.py#L2306-L2307 

Added lines #L2306 - L2307 were not covered by tests
elif var in self.symbols[SymbolId.SPECIES]:
sym_math = sym_math.subs(
var, self.symbols[SymbolId.SPECIES][var]["init"]
)
elif (
element := self.sbml.getElementBySId(element_id)
) and self.is_rate_rule_target(element):
# no need to recurse here, as value is numeric
init = sp.Float(element.getValue())
sym_math = sym_math.subs(var, init)

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python/sdist/amici/sbml_import.py#L2316-L2317 

Added lines #L2316 - L2317 were not covered by tests

sym_math = smart_subs(sym_math, sbml_time_symbol, sp.Float(0))

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130 changes: 130 additions & 0 deletions python/tests/sbml_models/regression_2642.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,130 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="debug" id="debug" substanceUnits="substance" timeUnits="time_unit" volumeUnits="volume" areaUnits="area" lengthUnits="length">
<listOfUnitDefinitions>
<unitDefinition id="length">
<listOfUnits>
<unit kind="metre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="area">
<listOfUnits>
<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time_unit" name="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="1" multiplier="6"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="-9" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="cytosol" spatialDimensions="3" size="0.0005" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="MR_i" compartment="cytosol" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="MR_m" compartment="cytosol" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="synthesis_MR" constant="true"/>
<parameter id="recycling" value="0.0000045" constant="true"/>
<parameter id="binding" constant="true"/>
<parameter id="MR_i_t0" value="1400000" constant="true"/>
<parameter id="MR_m_t0" value="600000" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="MR_i">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> MR_i_t0 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="MR_m">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> MR_m_t0 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="synthesis_MR">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<cn> 0.00585177319092733 </cn>
<cn> 0.00606 </cn>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="binding">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<minus/>
<apply>
<times/>
<ci> recycling </ci>
<ci> MR_i </ci>
</apply>
<ci> synthesis_MR </ci>
</apply>
<ci> MR_m </ci>
</apply>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfReactions>
<reaction id="_J0" reversible="true">
<listOfProducts>
<speciesReference species="MR_i" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> synthesis_MR </ci>
</math>
</kineticLaw>
</reaction>
<reaction id="_J1" reversible="true">
<listOfReactants>
<speciesReference species="MR_i" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="MR_m" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> recycling </ci>
<ci> MR_i </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="_J2" reversible="true">
<listOfReactants>
<speciesReference species="MR_m" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="MR_i" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> binding </ci>
<ci> MR_m </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
23 changes: 23 additions & 0 deletions python/tests/test_sbml_import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -852,3 +852,26 @@ def test_import_same_model_name():

assert model_module_1c.get_model().getParameters()[0] == 1.0
assert model_module_1c.get_model().module is model_module_1c


@skip_on_valgrind
def test_regression_2642():
sbml_file = Path(__file__).parent / "sbml_models" / "regression_2642.xml"
sbml_importer = amici.SbmlImporter(sbml_file)
model_name = "regression_2642"
with TemporaryDirectory(prefix="regression_2642") as outdir:
sbml_importer.sbml2amici(
model_name=model_name,
output_dir=outdir,
)
module = amici.import_model_module(
module_name=model_name, module_path=outdir
)
model = module.getModel()
solver = model.getSolver()
model.setTimepoints(np.linspace(0, 1, 3))
r = amici.runAmiciSimulation(model, solver)
assert (
len(np.unique(r.w[:, model.getExpressionIds().index("binding")]))
== 1
)
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