From c74bab4c0a8a709d0bc689e4d92323d00f1cf77a Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-munich.de>
Date: Tue, 2 Jul 2024 13:15:31 +0200
Subject: [PATCH] ..

---
 petabtests/cases/v1.0.0/sbml/0005/0005.py    | 24 ++++++-
 petabtests/cases/v1.0.0/sbml/0005/_model.xml | 69 ++++++--------------
 2 files changed, 41 insertions(+), 52 deletions(-)

diff --git a/petabtests/cases/v1.0.0/sbml/0005/0005.py b/petabtests/cases/v1.0.0/sbml/0005/0005.py
index 5676c9a..aae1ea4 100644
--- a/petabtests/cases/v1.0.0/sbml/0005/0005.py
+++ b/petabtests/cases/v1.0.0/sbml/0005/0005.py
@@ -4,7 +4,7 @@
 import pandas as pd
 from petab.v1.C import *
 
-from petabtests import PetabTestCase, analytical_a
+from petabtests import PetabTestCase, analytical_a, antimony_to_sbml_str
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -23,6 +23,26 @@
 """)
 
 # problem --------------------------------------------------------------------
+ant_model = """
+model *petab_test_0011()
+  compartment compartment_ = 1;
+  species A in compartment_, B in compartment_;
+
+  fwd: A => B; compartment_ * k1 * A;
+  rev: B => A; compartment_ * k2 * B;
+
+  A = a0;
+  B = b0;
+  B = 1;
+  a0 = 1;
+  b0 = 1;
+  k1 = 0;
+  k2 = 0;
+  offset_A = 0;
+end
+"""
+model_file = sbml_file = Path(__file__).parent / "_model.xml"
+model_file.write_text(antimony_to_sbml_str(ant_model))
 
 condition_df = pd.DataFrame(
     data={
@@ -73,7 +93,7 @@
     brief="Simulation. Condition-specific parameters only defined in "
     "parameter table.",
     description=DESCRIPTION,
-    model=Path("conversion_modified.xml"),
+    model=model_file,
     condition_dfs=[condition_df],
     observable_dfs=[observable_df],
     measurement_dfs=[measurement_df],
diff --git a/petabtests/cases/v1.0.0/sbml/0005/_model.xml b/petabtests/cases/v1.0.0/sbml/0005/_model.xml
index 95e0fcb..5e9270a 100644
--- a/petabtests/cases/v1.0.0/sbml/0005/_model.xml
+++ b/petabtests/cases/v1.0.0/sbml/0005/_model.xml
@@ -1,89 +1,59 @@
 <?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>
-
+<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="petab_test_0011" id="petab_test_0011">
     <listOfCompartments>
-      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
-      </compartment>
+      <compartment id="compartment_" spatialDimensions="3" size="1" constant="true"/>
     </listOfCompartments>
-
     <listOfSpecies>
-      <species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
-      </species>
-      <species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
-      </species>
+      <species id="A" compartment="compartment_" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="B" compartment="compartment_" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </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>
-      <parameter id="offset_A" name="offset_A" value="0" constant="true">
-      </parameter>
+      <parameter id="k1" value="0" constant="true"/>
+      <parameter id="k2" value="0" constant="true"/>
+      <parameter id="a0" value="1" constant="true"/>
+      <parameter id="b0" value="1" constant="true"/>
+      <parameter id="offset_A" value="0" constant="true"/>
     </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">
+      <reaction id="fwd" reversible="false">
         <listOfReactants>
-          <speciesReference species="A" stoichiometry="1"/>
+          <speciesReference species="A" stoichiometry="1" constant="true"/>
         </listOfReactants>
         <listOfProducts>
-          <speciesReference species="B" stoichiometry="1"/>
+          <speciesReference species="B" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
-              <ci> compartment </ci>
+              <ci> compartment_ </ci>
               <ci> k1 </ci>
               <ci> A </ci>
             </apply>
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="rev" name="rev" reversible="false">
+      <reaction id="rev" reversible="false">
         <listOfReactants>
-          <speciesReference species="B" stoichiometry="1"/>
+          <speciesReference species="B" stoichiometry="1" constant="true"/>
         </listOfReactants>
         <listOfProducts>
-          <speciesReference species="A" stoichiometry="1"/>
+          <speciesReference species="A" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
-              <ci> compartment </ci>
+              <ci> compartment_ </ci>
               <ci> k2 </ci>
               <ci> B </ci>
             </apply>
@@ -91,6 +61,5 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-
   </model>
 </sbml>