Merge branch 'main' into doc

PEtab-dev · Jul 2, 2024 · 6eabe70 · 6eabe70
2 parents 6969f2e + 3d0bc1b
commit 6eabe70
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diff --git a/petabtests/__init__.py b/petabtests/__init__.py
@@ -6,3 +6,4 @@
 from .file import *  # noqa: F403, F401
 from .evaluate import *  # noqa: F403, F401
 from .core import *  # noqa: F403, F401
+from .antimony import *  # noqa: F403, F401
diff --git a/petabtests/antimony.py b/petabtests/antimony.py
@@ -0,0 +1,40 @@
+"""Antimony -> SBML"""
+
+import antimony as ant
+from pathlib import Path
+
+__all__ = ["antimony_to_sbml_str"]
+
+
+def antimony_to_sbml_str(ant_model: str | Path) -> str:
+    """Convert Antimony string to SBML model.
+
+    Arguments:
+        ant_str:
+            Antimony model as string (model, not filename), or Path to file.
+
+    Returns:
+        SBML model as string.
+    """
+
+    # Unload everything / free memory
+    ant.clearPreviousLoads()
+    ant.freeAll()
+
+    if isinstance(ant_model, Path):
+        status = ant.loadAntimonyFile(str(ant_model))
+    else:
+        status = ant.loadAntimonyString(ant_model)
+    if status < 0:
+        raise RuntimeError(
+            f"Antimony model could not be loaded: {ant.getLastError()}"
+        )
+
+    if (main_module_name := ant.getMainModuleName()) is None:
+        raise AssertionError("There is no Antimony module.")
+
+    sbml_str = ant.getSBMLString(main_module_name)
+    if not sbml_str:
+        raise ValueError("Antimony model could not be converted to SBML.")
+
+    return sbml_str
diff --git a/petabtests/cases/v1.0.0/sbml/0018/0018.py b/petabtests/cases/v1.0.0/sbml/0018/0018.py
@@ -3,7 +3,12 @@
 import pandas as pd
 from petab.v1.C import *
 from pathlib import Path
-from petabtests import PetabTestCase, analytical_a, analytical_b
+from petabtests import (
+    PetabTestCase,
+    analytical_a,
+    analytical_b,
+    antimony_to_sbml_str,
+)
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -28,30 +33,23 @@
 
 # problem --------------------------------------------------------------------
 
-model = str(Path(__file__).parent / "model.xml")
-
-
-def get_model():
-    import simplesbml
-
-    model = simplesbml.SbmlModel()
-    model.addParameter("a0", 1)
-    model.addParameter("b0", 1)
-    model.addParameter("k1", 0)
-    model.addParameter("k2", 0)
-    model.addCompartment(comp_id="compartment")
-    model.addSpecies("[A]", 0, comp="compartment")
-    model.addParameter("B", 0)
-    model.addInitialAssignment("A", "a0")
-    model.addInitialAssignment("B", "b0")
-    model.addRateRule("A", "k2 * B - k1 * A")
-    model.addRateRule("B", "- compartment * k2 * B + compartment * k1 * A")
-    return model
-
+sbml_file = Path(__file__).parent / "model.xml"
 
-with open(model, "w") as f:
-    f.write(get_model().toSBML())
 
+ant_model = """
+model petab_test_0018
+    a0 = 1
+    b0 = 1
+    k1 = 0
+    k2 = 0
+    compartment default_compartment
+    species A in default_compartment = a0
+    B = b0
+    A' = k2 * B - k1 * A
+    B' = - default_compartment * k2 * B + default_compartment * k1 * A
+end
+"""
+sbml_file.write_text(antimony_to_sbml_str(ant_model))
 
 condition_df = pd.DataFrame(
     data={
@@ -114,7 +112,7 @@ def get_model():
     "reinitialized, one not (NaN in condition table). InitialAssignment "
     "to species overridden.",
     description=DESCRIPTION,
-    model=model,
+    model=sbml_file,
     condition_dfs=[condition_df],
     observable_dfs=[observable_df],
     measurement_dfs=[measurement_df],

diff --git a/petabtests/cases/v1.0.0/sbml/0018/_model.xml b/petabtests/cases/v1.0.0/sbml/0018/_model.xml
@@ -1,26 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
-  <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
-    <listOfUnitDefinitions>
-      <unitDefinition id="per_second">
-        <listOfUnits>
-          <unit kind="second" exponent="-1" scale="0" 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_0018" id="petab_test_0018">
     <listOfCompartments>
-      <compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
-      <compartment id="compartment" spatialDimensions="3" size="1" units="litre" constant="true"/>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="A" compartment="compartment" initialConcentration="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="A" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="a0" value="1" units="per_second" constant="false"/>
-      <parameter id="b0" value="1" units="per_second" constant="false"/>
-      <parameter id="k1" value="0" units="per_second" constant="false"/>
-      <parameter id="k2" value="0" units="per_second" constant="false"/>
-      <parameter id="B" value="0" units="per_second" constant="false"/>
+      <parameter id="a0" value="1" constant="true"/>
+      <parameter id="b0" value="1" constant="true"/>
+      <parameter id="k1" value="0" constant="true"/>
+      <parameter id="k2" value="0" constant="true"/>
+      <parameter id="B" constant="false"/>
     </listOfParameters>
     <listOfInitialAssignments>
       <initialAssignment symbol="A">
@@ -60,14 +53,14 @@
               <times/>
               <apply>
                 <minus/>
-                <ci> compartment </ci>
+                <ci> default_compartment </ci>
               </apply>
               <ci> k2 </ci>
               <ci> B </ci>
             </apply>
             <apply>
               <times/>
-              <ci> compartment </ci>
+              <ci> default_compartment </ci>
               <ci> k1 </ci>
               <ci> A </ci>
             </apply>

diff --git a/petabtests/cases/v1.0.0/sbml/0018/model.xml b/petabtests/cases/v1.0.0/sbml/0018/model.xml
@@ -1,26 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
-  <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
-    <listOfUnitDefinitions>
-      <unitDefinition id="per_second">
-        <listOfUnits>
-          <unit kind="second" exponent="-1" scale="0" 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_0018" id="petab_test_0018">
     <listOfCompartments>
-      <compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
-      <compartment id="compartment" spatialDimensions="3" size="1" units="litre" constant="true"/>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="A" compartment="compartment" initialConcentration="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="A" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="a0" value="1" units="per_second" constant="false"/>
-      <parameter id="b0" value="1" units="per_second" constant="false"/>
-      <parameter id="k1" value="0" units="per_second" constant="false"/>
-      <parameter id="k2" value="0" units="per_second" constant="false"/>
-      <parameter id="B" value="0" units="per_second" constant="false"/>
+      <parameter id="a0" value="1" constant="true"/>
+      <parameter id="b0" value="1" constant="true"/>
+      <parameter id="k1" value="0" constant="true"/>
+      <parameter id="k2" value="0" constant="true"/>
+      <parameter id="B" constant="false"/>
     </listOfParameters>
     <listOfInitialAssignments>
       <initialAssignment symbol="A">
@@ -60,14 +53,14 @@
               <times/>
               <apply>
                 <minus/>
-                <ci> compartment </ci>
+                <ci> default_compartment </ci>
               </apply>
               <ci> k2 </ci>
               <ci> B </ci>
             </apply>
             <apply>
               <times/>
-              <ci> compartment </ci>
+              <ci> default_compartment </ci>
               <ci> k1 </ci>
               <ci> A </ci>
             </apply>

diff --git a/petabtests/cases/v2.0.0/sbml/0018/0018.py b/petabtests/cases/v2.0.0/sbml/0018/0018.py
@@ -3,7 +3,12 @@
 import pandas as pd
 from petab.v1.C import *
 from pathlib import Path
-from petabtests import PetabTestCase, analytical_a, analytical_b
+from petabtests import (
+    PetabTestCase,
+    analytical_a,
+    analytical_b,
+    antimony_to_sbml_str,
+)
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -28,30 +33,22 @@
 
 # problem --------------------------------------------------------------------
 
-model = str(Path(__file__).parent / "model.xml")
-
-
-def get_model():
-    import simplesbml
-
-    model = simplesbml.SbmlModel()
-    model.addParameter("a0", 1)
-    model.addParameter("b0", 1)
-    model.addParameter("k1", 0)
-    model.addParameter("k2", 0)
-    model.addCompartment(comp_id="compartment")
-    model.addSpecies("[A]", 0, comp="compartment")
-    model.addParameter("B", 0)
-    model.addInitialAssignment("A", "a0")
-    model.addInitialAssignment("B", "b0")
-    model.addRateRule("A", "k2 * B - k1 * A")
-    model.addRateRule("B", "- compartment * k2 * B + compartment * k1 * A")
-    return model
-
-
-with open(model, "w") as f:
-    f.write(get_model().toSBML())
-
+sbml_file = Path(__file__).parent / "model.xml"
+
+ant_model = """
+model petab_test_0018
+    a0 = 1
+    b0 = 1
+    k1 = 0
+    k2 = 0
+    compartment default_compartment
+    species A in default_compartment = a0
+    B = b0
+    A' = k2 * B - k1 * A
+    B' = - default_compartment * k2 * B + default_compartment * k1 * A
+end
+"""
+sbml_file.write_text(antimony_to_sbml_str(ant_model))
 
 condition_df = pd.DataFrame(
     data={
@@ -114,7 +111,7 @@ def get_model():
     "reinitialized, one not (NaN in condition table). InitialAssignment "
     "to species overridden.",
     description=DESCRIPTION,
-    model=model,
+    model=sbml_file,
     condition_dfs=[condition_df],
     observable_dfs=[observable_df],
     measurement_dfs=[measurement_df],

diff --git a/petabtests/cases/v2.0.0/sbml/0018/_model.xml b/petabtests/cases/v2.0.0/sbml/0018/_model.xml
@@ -1,26 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
-  <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
-    <listOfUnitDefinitions>
-      <unitDefinition id="per_second">
-        <listOfUnits>
-          <unit kind="second" exponent="-1" scale="0" 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_0018" id="petab_test_0018">
     <listOfCompartments>
-      <compartment id="c1" spatialDimensions="3" size="1" units="litre" constant="true"/>
-      <compartment id="compartment" spatialDimensions="3" size="1" units="litre" constant="true"/>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="A" compartment="compartment" initialConcentration="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="A" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="a0" value="1" units="per_second" constant="false"/>
-      <parameter id="b0" value="1" units="per_second" constant="false"/>
-      <parameter id="k1" value="0" units="per_second" constant="false"/>
-      <parameter id="k2" value="0" units="per_second" constant="false"/>
-      <parameter id="B" value="0" units="per_second" constant="false"/>
+      <parameter id="a0" value="1" constant="true"/>
+      <parameter id="b0" value="1" constant="true"/>
+      <parameter id="k1" value="0" constant="true"/>
+      <parameter id="k2" value="0" constant="true"/>
+      <parameter id="B" constant="false"/>
     </listOfParameters>
     <listOfInitialAssignments>
       <initialAssignment symbol="A">
@@ -60,14 +53,14 @@
               <times/>
               <apply>
                 <minus/>
-                <ci> compartment </ci>
+                <ci> default_compartment </ci>
               </apply>
               <ci> k2 </ci>
               <ci> B </ci>
             </apply>
             <apply>
               <times/>
-              <ci> compartment </ci>
+              <ci> default_compartment </ci>
               <ci> k1 </ci>
               <ci> A </ci>
             </apply>