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Add test triggered at time-point without measurements (#105)
Unlike the other test cases with non-initial PEtab conditions (`0016` and `0022`), this test case includes a condition that is triggered at a time point without any measurement values. I have confirmed that the output matches what is computed by PEtab.jl. I believe this is important to test because many ODE solver libraries, unless configured otherwise, save model output immediately after an event/callback (e.g., diffrax in Jax). In this test, that behavior is not required, and if an importer always saves model output following a PEtab condition event, this test case may cause indexing issues when computing the model output. * Add test for unbounded priors * Add test case triggered at time-point without measurements * Use default SBML model * Fix style
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‎petabtests/cases/v2.0.0/sbml/0028/0028.py‎

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from inspect import cleandoc
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from petab.v2.C import *
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from petab.v2 import Problem
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from petabtests import PetabV2TestCase, analytical_a, analytical_b, DEFAULT_SBML_FILE
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DESCRIPTION = cleandoc("""
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## Objective
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This case tests applies a PEtab condition at a non-initial time point,
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where the condition is triggered at a time point that does not have any
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measurements.
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## Model
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A simple conversion reaction `A <=> B` in a single compartment, following
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mass action kinetics.
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""")
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# problem --------------------------------------------------------------------
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a0 = 1
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b0 = 1
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k1 = 0.8
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k2 = 0.6
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problem = Problem()
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problem.add_condition(
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"condition1",
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"condition1",
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A="A + 5.0",
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)
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problem.add_experiment("experiment1", 0, "", 7, "condition1")
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problem.add_observable("obs_a", "A", noise_formula="0.5")
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problem.add_measurement("obs_a", experiment_id="experiment1", time=0, measurement=0.7)
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problem.add_measurement("obs_a", experiment_id="experiment1", time=10, measurement=0.1)
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problem.add_parameter("k1", lb=0, ub=10, nominal_value=k1, estimate=True)
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problem.add_parameter("k2", lb=0, ub=10, nominal_value=k2, estimate=True)
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# solutions ------------------------------------------------------------------
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simulation_df = problem.measurement_df.copy(deep=True).rename(
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columns={MEASUREMENT: SIMULATION}
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)
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# in the model, concentrations are used, which do not depend on the
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# compartment size, so that the species values should stay the same
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a7 = analytical_a(7.0, a0=a0, b0=b0, k1=k1, k2=k2)
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b7 = analytical_b(7.0, a0=a0, b0=b0, k1=k1, k2=k2)
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simulation_df[SIMULATION] = [
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a0,
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analytical_a(3.0, a0=(a7 + 5.0), b0=b7, k1=k1, k2=k2)
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]
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case = PetabV2TestCase.from_problem(
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id=28,
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brief="Simulation. None t0 condition applied at time-point "
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"without measurements.",
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description=DESCRIPTION,
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model=DEFAULT_SBML_FILE,
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problem=problem,
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simulation_df=simulation_df,
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)

‎petabtests/cases/v2.0.0/sbml/0028/README.md‎

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# PEtab test case 0028
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## Objective
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This case tests applies a PEtab condition at a non-initial time point,
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where the condition is triggered at a time point that does not have any
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measurements.
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## Model
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A simple conversion reaction `A <=> B` in a single compartment, following
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mass action kinetics.

‎petabtests/cases/v2.0.0/sbml/0028/_0028.yaml‎

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condition_files:
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- _conditions.tsv
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experiment_files:
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- _experiments.tsv
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format_version: 2.0.0
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mapping_files:
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- _mapping.tsv
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measurement_files:
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- _measurements.tsv
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model_files:
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model_0:
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language: sbml
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location: _model.xml
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observable_files:
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- _observables.tsv
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parameter_files:
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- _parameters.tsv

‎petabtests/cases/v2.0.0/sbml/0028/_0028_solution.yaml‎

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chi2: 35.00133792381521
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llh: -17.95225166719706
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simulation_files:
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- _simulations.tsv
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tol_chi2: 0.001
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tol_llh: 0.001
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tol_simulations: 0.001

‎petabtests/cases/v2.0.0/sbml/0028/_conditions.tsv‎

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conditionId targetId targetValue
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condition1 A A + 5.0

‎petabtests/cases/v2.0.0/sbml/0028/_experiments.tsv‎

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experimentId time conditionId
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experiment1 0.0
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experiment1 7.0 condition1

‎petabtests/cases/v2.0.0/sbml/0028/_mapping.tsv‎

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petabEntityId modelEntityId name
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condition1 condition1

‎petabtests/cases/v2.0.0/sbml/0028/_measurements.tsv‎

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modelId observableId experimentId time measurement observableParameters noiseParameters
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obs_a experiment1 0.0 0.7
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obs_a experiment1 10.0 0.1

‎petabtests/cases/v2.0.0/sbml/0028/_model.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
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<model id="conversion_reaction_0" name="Conversion Reaction 0">
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<listOfUnitDefinitions>
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<unitDefinition id="volume" name="volume">
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="substance" name="substance">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species id="A" name="A" compartment="compartment" initialConcentration="2" boundaryCondition="false" constant="false">
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</species>
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<species id="B" name="B" compartment="compartment" initialConcentration="2" boundaryCondition="false" constant="false">
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="a0" name="a0" value="1" constant="true">
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</parameter>
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<parameter id="b0" name="b0" value="1" constant="true">
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</parameter>
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<parameter id="k1" name="k1" value="0" constant="true">
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</parameter>
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<parameter id="k2" name="k2" value="0" constant="true">
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</parameter>
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</listOfParameters>
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<listOfInitialAssignments>
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<initialAssignment symbol="A">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> a0 </ci>
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</math>
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</initialAssignment>
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<initialAssignment symbol="B">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> b0 </ci>
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</math>
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</initialAssignment>
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</listOfInitialAssignments>
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<listOfReactions>
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<reaction id="fwd" name="fwd" reversible="false">
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<listOfReactants>
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<speciesReference species="A" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="B" stoichiometry="1"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> k1 </ci>
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<ci> A </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction id="rev" name="rev" reversible="false">
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<listOfReactants>
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<speciesReference species="B" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="A" stoichiometry="1"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> k2 </ci>
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<ci> B </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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</model>
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</sbml>

‎petabtests/cases/v2.0.0/sbml/0028/_observables.tsv‎

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observableId observableName observableFormula noiseFormula noiseDistribution observablePlaceholders noisePlaceholders
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obs_a A 0.500000000000000 normal

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