Add SbmlModel.{to_antimony,to_sbml_str} (#371)

Simplify conversion of SBML models to antimony and XML strings. Convenient in particular for debugging.

Author: dweindl

petab/v1/models/sbml_model.py

@@ -65,9 +65,7 @@ def __getstate__(self):
 
         # libsbml stuff cannot be serialized directly
         if self.sbml_model:
-            sbml_document = self.sbml_model.getSBMLDocument()
-            sbml_writer = libsbml.SBMLWriter()
-            state["sbml_string"] = sbml_writer.writeSBMLToString(sbml_document)
+            state["sbml_string"] = self.to_sbml_str()
 
         exclude = ["sbml_reader", "sbml_document", "sbml_model"]
         for key in exclude:
@@ -133,6 +131,26 @@ def from_antimony(ant_model: str | Path) -> SbmlModel:
         sbml_str = antimony2sbml(ant_model)
         return SbmlModel.from_string(sbml_str)
 
+    def to_antimony(self) -> str:
+        """Convert the SBML model to an Antimony string."""
+        import antimony as ant
+
+        sbml_str = self.to_sbml_str()
+
+        ant.clearPreviousLoads()
+        ant.freeAll()
+
+        if ant.loadSBMLString(sbml_str) < 0:
+            raise RuntimeError(ant.getLastError())
+
+        return ant.getAntimonyString()
+
+    def to_sbml_str(self) -> str:
+        """Convert the SBML model to an SBML/XML string."""
+        sbml_document = self.sbml_model.getSBMLDocument()
+        sbml_writer = libsbml.SBMLWriter()
+        return sbml_writer.writeSBMLToString(sbml_document)
+
     @property
     def model_id(self):
         return self._model_id

tests/v1/test_sbml.py

@@ -134,7 +134,7 @@ def test_sbml_model_repr():
     assert repr(petab_model) == "<SbmlModel 'test'>"
 
 
-def test_sbml_from_ant():
+def test_sbml_from_to_ant():
     ant_model = """
     model test
         R1: S1 -> S2; k1*S1
@@ -147,3 +147,6 @@ def test_sbml_from_ant():
     assert set(petab_model.get_valid_parameters_for_parameter_table()) == {
         "k1"
     }
+
+    # convert back to antimony
+    assert "R1: S1 -> S2; k1*S1" in petab_model.to_antimony()