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Fix handling of initial assignments containing splines #2943

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Merged
dweindl merged 1 commit into from
Aug 29, 2025
Merged

Fix handling of initial assignments containing splines #2943

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16 changes: 14 additions & 2 deletions python/sdist/amici/sbml_import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1526,14 +1526,14 @@ def _process_rules(self) -> None:
self.symbols[SymbolId.EXPRESSION], "value"
)

# expressions must not occur in the definition of x0
# substitute symbols that must not occur in the definition of x0
# allowed symbols: amici model parameters and time
allowed_syms = (
set(self.symbols[SymbolId.PARAMETER])
| set(self.symbols[SymbolId.FIXED_PARAMETER])
| {sbml_time_symbol}
)
for species in self.symbols[SymbolId.SPECIES].values():
# only parameters are allowed as free symbols
while True:
species["init"] = species["init"].subs(self.compartments)
sym_math, rateof_to_dummy = _rateof_to_dummy(species["init"])
Expand Down Expand Up @@ -2403,6 +2403,18 @@ def _make_initial(
# no need to recurse here, as value is numeric
init = sp.Float(element.getValue())
sym_math = sym_math.subs(var, init)
elif spline := [spl for spl in self.splines if spl.sbml_id == var]:
# x0 must not depend on splines -- substitute
assert len(spline) == 1
spline = spline[0]
if spline.evaluate_at != sbml_time_symbol:
raise NotImplementedError(
"AMICI at the moment does not support splines "
"whose evaluation point is not the model time."
)
sym_math = sym_math.subs(
var, spline.evaluate(sbml_time_symbol)
)

sym_math = _dummy_to_rateof(sym_math, rateof_to_dummy)

Expand Down
25 changes: 22 additions & 3 deletions python/tests/test_sbml_import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1150,6 +1150,7 @@ def test_time_dependent_initial_assignment(compute_conservation_laws: bool):
"""Check that dynamic expressions for initial assignments are only
evaluated at t=t0."""
from amici.antimony_import import antimony2sbml
from amici.import_utils import amici_time_symbol

ant_model = """
x1' = 1
Expand All @@ -1158,10 +1159,23 @@ def test_time_dependent_initial_assignment(compute_conservation_laws: bool):
p1 = x1
x2 := x1
p2 = x2
spline1 = 0 # replaced by actual spline below
x3' = 0
x3 = spline1
"""
sbml_str = antimony2sbml(ant_model)
sbml_reader = libsbml.SBMLReader()
sbml_document = sbml_reader.readSBMLFromString(sbml_str)
sbml_model = sbml_document.getModel()

spline = amici.splines.CubicHermiteSpline(
sbml_id="spline1",
nodes=[0, 1, 2],
values_at_nodes=[3, 4, 5],
)
spline.add_to_sbml_model(sbml_model)
sbml_model.getElementBySId("spline1").setConstant(False)

sbml_model = antimony2sbml(ant_model)
print(sbml_model)
si = SbmlImporter(sbml_model, from_file=False)
de_model = si._build_ode_model(
observables={"obs_p1": {"formula": "p1"}, "obs_p2": {"formula": "p2"}},
Expand All @@ -1179,5 +1193,10 @@ def test_time_dependent_initial_assignment(compute_conservation_laws: bool):
assert list(de_model.sym("x_rdata")) == [
symbol_with_assumptions("p2"),
symbol_with_assumptions("x1"),
symbol_with_assumptions("x3"),
]
assert list(de_model.eq("x0")) == [
symbol_with_assumptions("p0"),
symbol_with_assumptions("p0"),
amici_time_symbol * 1.0 + 3.0,
]
assert list(de_model.eq("x0")) == [symbol_with_assumptions("p0")] * 2
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