ExperimentsToSbmlConverter nests initial-assignment Piecewise once per experiment, exceeding lxml's depth limit #540

expr = sp.Piecewise(*expr_cond_pairs, (default, True))

import sys
import tempfile
from pathlib import Path

import libsbml
from petab.v2 import Problem
from petab.v2.converters import ExperimentsToSbmlConverter

N = int(sys.argv[1])  # number of conditions setting the initial value of A
d = Path(tempfile.mkdtemp())
doc = libsbml.readSBMLFromString(
    """<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
  <model id="m">
    <listOfCompartments><compartment id="C" size="1" constant="true"/></listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="C" initialAmount="1" hasOnlySubstanceUnits="false"
               boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters><parameter id="k" value="1" constant="true"/></listOfParameters>
  </model>
</sbml>"""
)
libsbml.writeSBMLToFile(doc, str(d / "model.xml"))
(d / "conditions.tsv").write_text(
    "conditionId\tA\n" + "".join(f"c{i}\t{i + 1}\n" for i in range(N))
)
(d / "observables.tsv").write_text(
    "observableId\tobservableFormula\tnoiseFormula\nobs_A\tA\t1\n"
)
(d / "measurements.tsv").write_text(
    "observableId\tsimulationConditionId\ttime\tmeasurement\n"
    + "".join(f"obs_A\tc{i}\t1\t1\n" for i in range(N))
)
(d / "parameters.tsv").write_text(
    "parameterId\tparameterScale\tlowerBound\tupperBound\tnominalValue\testimate\n"
    "k\tlin\t0\t10\t1\t1\n"
)
(d / "problem.yaml").write_text(
    "format_version: 1\nparameter_file: parameters.tsv\nproblems:\n"
    "- sbml_files: [model.xml]\n  condition_files: [conditions.tsv]\n"
    "  measurement_files: [measurements.tsv]\n  observable_files: [observables.tsv]\n"
)

problem = Problem.from_yaml(d / "problem.yaml")  # upgraded from PEtab v1
converted = ExperimentsToSbmlConverter(problem).convert()
model = converted.model.sbml_model
math = model.getInitialAssignmentBySymbol("A").getMath()


def depth(node):
    return 1 + max((depth(node.getChild(i)) for i in range(node.getNumChildren())), default=0)


print(f"{N} conditions: initial assignment of A nests {depth(math)} levels deep")