Fix v1.0.0/sbml/0005

PEtab-dev · Jul 2, 2024 · b4cc51a · b4cc51a
1 parent bd0ff4d
commit b4cc51a
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Showing 5 changed files with 18 additions and 9 deletions.
diff --git a/petabtests/cases/v1.0.0/sbml/0005/0005.py b/petabtests/cases/v1.0.0/sbml/0005/0005.py
@@ -33,7 +33,6 @@
 
   A = a0;
   B = b0;
-  B = 1;
   a0 = 1;
   b0 = 1;
   k1 = 0;
@@ -53,10 +52,10 @@
 
 measurement_df = pd.DataFrame(
     data={
-        OBSERVABLE_ID: ["obs_a", "obs_a"],
-        SIMULATION_CONDITION_ID: ["c0", "c1"],
-        TIME: [10, 10],
-        MEASUREMENT: [2.1, 3.2],
+        OBSERVABLE_ID: ["obs_a", "obs_a", "obs_a", "obs_a"],
+        SIMULATION_CONDITION_ID: ["c0", "c1", "c0", "c1"],
+        TIME: [0, 0, 10, 10],
+        MEASUREMENT: [2.0, 2.0, 2.1, 3.2],
     }
 )
 
@@ -85,7 +84,8 @@
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
-    analytical_a(10, 1, 0, 0.8, 0.6) + offset for offset in [2, 3]
+    *(analytical_a(0, 1, 0, 0.8, 0.6) + offset for offset in [2, 3]),
+    *(analytical_a(10, 1, 0, 0.8, 0.6) + offset for offset in [2, 3]),
 ]
 
 case = PetabTestCase(

diff --git a/petabtests/cases/v1.0.0/sbml/0005/_0005_solution.yaml b/petabtests/cases/v1.0.0/sbml/0005/_0005_solution.yaml
@@ -1,5 +1,5 @@
-chi2: 0.16020461109629
-llh: -1.91797937195749
+chi2: 5.16020461109629
+llh: -6.25585643836683
 simulation_files:
 - _simulations.tsv
 tol_chi2: 0.001

diff --git a/petabtests/cases/v1.0.0/sbml/0005/_measurements.tsv b/petabtests/cases/v1.0.0/sbml/0005/_measurements.tsv
@@ -1,3 +1,5 @@
 observableId	simulationConditionId	time	measurement
+obs_a	c0	0	2.0
+obs_a	c1	0	2.0
 obs_a	c0	10	2.1
 obs_a	c1	10	3.2
diff --git a/petabtests/cases/v1.0.0/sbml/0005/_model.xml b/petabtests/cases/v1.0.0/sbml/0005/_model.xml
@@ -7,7 +7,7 @@
     </listOfCompartments>
     <listOfSpecies>
       <species id="A" compartment="compartment_" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-      <species id="B" compartment="compartment_" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="B" compartment="compartment_" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
     <listOfParameters>
       <parameter id="k1" value="0" constant="true"/>
@@ -22,6 +22,11 @@
           <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" reversible="false">

diff --git a/petabtests/cases/v1.0.0/sbml/0005/_simulations.tsv b/petabtests/cases/v1.0.0/sbml/0005/_simulations.tsv
@@ -1,3 +1,5 @@
 observableId	simulationConditionId	time	simulation
+obs_a	c0	0	3.0
+obs_a	c1	0	4.0
 obs_a	c0	10	2.4285719037306968
 obs_a	c1	10	3.4285719037306968