Test case with non zero start time

petabtests/cases/v2.0.0/sbml/0018/0018.py

@@ -22,6 +22,9 @@
 `A` is reinitialized to the value in the condition table after
 preequilibration, `B` is not updated.
 
+This test is a more tricky version of test 0029, which also includes a
+non-zero simulation start time without a preequilibration condition.
+
 ## Model
 
 A simple conversion reaction `A <=> B` in a single compartment, following

petabtests/cases/v2.0.0/sbml/0018/README.md

@@ -11,6 +11,9 @@ For preequilibration, species `B` is initialized with `0`. For simulation,
 `A` is reinitialized to the value in the condition table after
 preequilibration, `B` is not updated.
 
+This test is a more tricky version of test 0029, which also includes a
+non-zero simulation start time without a preequilibration condition.
+
 ## Model
 
 A simple conversion reaction `A <=> B` in a single compartment, following

petabtests/cases/v2.0.0/sbml/0029/0029.py

@@ -0,0 +1,54 @@
+from inspect import cleandoc
+
+from petab.v2.C import *
+from petab.v2.core import *
+from petab.v2 import Problem
+from petabtests import DEFAULT_SBML_FILE, PetabV2TestCase, analytical_a
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case features a simple test with two data points with a non-zero
+simulation start time.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+a0 = 1.0
+b0 = 1.0
+k1 = 0.8
+k2 = 0.6
+
+problem = Problem()
+problem.add_experiment("e1", 5.0, "")
+
+problem.add_observable("obs_a", "A", noise_formula="1")
+
+problem.add_measurement("obs_a", experiment_id="e1", time=5, measurement=0.01)
+problem.add_measurement("obs_a", experiment_id="e1", time=10, measurement=0.1)
+
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=k1, estimate=True)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=k2, estimate=True)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = problem.measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    analytical_a(t=(t - 5.0), a0=a0, b0=b0, k1=k1, k2=k2) for t in simulation_df[TIME]
+]
+
+
+case = PetabV2TestCase.from_problem(
+    id=29,
+    problem=problem,
+    brief="Simulation. Non-zero simulation start time",
+    description=DESCRIPTION,
+    model=DEFAULT_SBML_FILE,
+    simulation_df=simulation_df,
+)

petabtests/cases/v2.0.0/sbml/0029/README.md

@@ -0,0 +1,11 @@
+# PEtab test case 0029
+
+## Objective
+
+This case features a simple test with two data points with a non-zero
+simulation start time.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.

petabtests/cases/v2.0.0/sbml/0029/_0029.yaml

@@ -0,0 +1,14 @@
+condition_files: []
+experiment_files:
+- _experiments.tsv
+format_version: 2.0.0
+measurement_files:
+- _measurements.tsv
+model_files:
+  model_0:
+    language: sbml
+    location: _model.xml
+observable_files:
+- _observables.tsv
+parameter_files:
+- _parameters.tsv

petabtests/cases/v2.0.0/sbml/0029/_0029_solution.yaml

@@ -0,0 +1,7 @@
+chi2: 1.55356258735436
+llh: -2.61465836008652
+simulation_files:
+- _simulations.tsv
+tol_chi2: 0.001
+tol_llh: 0.001
+tol_simulations: 0.001

petabtests/cases/v2.0.0/sbml/0029/_experiments.tsv

@@ -0,0 +1,2 @@
+experimentId	time	conditionId
+e1	5.0	

petabtests/cases/v2.0.0/sbml/0029/_measurements.tsv

@@ -0,0 +1,3 @@
+modelId	observableId	experimentId	time	measurement	observableParameters	noiseParameters
+	obs_a	e1	5.0	0.01		
+	obs_a	e1	10.0	0.1		

petabtests/cases/v2.0.0/sbml/0029/_model.xml

@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="conversion_reaction_0" name="Conversion Reaction 0">
+
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume" name="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance" name="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
+      </compartment>
+    </listOfCompartments>
+
+    <listOfSpecies>
+      <species id="A" name="A" compartment="compartment" initialConcentration="2" boundaryCondition="false" constant="false">
+      </species>
+      <species id="B" name="B" compartment="compartment" initialConcentration="2" boundaryCondition="false" constant="false">
+      </species>
+    </listOfSpecies>
+
+    <listOfParameters>
+      <parameter id="a0" name="a0" value="1" constant="true">
+      </parameter>
+      <parameter id="b0" name="b0" value="1" constant="true">
+      </parameter>
+      <parameter id="k1" name="k1" value="0" constant="true">
+      </parameter>
+      <parameter id="k2" name="k2" value="0" constant="true">
+      </parameter>
+    </listOfParameters>
+
+    <listOfInitialAssignments>
+      <initialAssignment symbol="A">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> a0 </ci>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="B">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> b0 </ci>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+
+    <listOfReactions>
+      <reaction id="fwd" name="fwd" reversible="false">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="rev" name="rev" reversible="false">
+        <listOfReactants>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k2 </ci>
+              <ci> B </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+
+  </model>
+</sbml>

petabtests/cases/v2.0.0/sbml/0029/_observables.tsv

@@ -0,0 +1,2 @@
+observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
+obs_a		A	1.00000000000000	normal		

petabtests/cases/v2.0.0/sbml/0029/_parameters.tsv

@@ -0,0 +1,3 @@
+parameterId	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
+k1	0.0	10.0	0.8	true		
+k2	0.0	10.0	0.6	true		

petabtests/cases/v2.0.0/sbml/0029/_simulations.tsv

@@ -0,0 +1,3 @@
+modelId	observableId	experimentId	time	simulation	observableParameters	noiseParameters
+	obs_a	e1	5.0	1.0		
+	obs_a	e1	10.0	0.8572731259950793		

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

@@ -106,3 +106,7 @@ Simulation. Condition-specific parameters defined via math expressions in the pa
 
 Simulation. None t0 condition applied at time-point without measurements.
 
+# [0029](0029/)
+
+Simulation. Non-zero simulation start time
+