fix units not recognized

pyenzyme/sbml/serializer.py

@@ -67,7 +67,10 @@ def to_sbml(
     sbmldoc = libsbml.SBMLDocument()
     model = sbmldoc.createModel()
     model.setName(doc.name)
-    units = _assign_ids_to_units(tools.find_unique(doc, UnitDefinition))
+    units = _assign_ids_to_units(tools.find_unique(doc, pe.UnitDefinition))
+
+    # Add units that have been defined by the custom UnitDefinition
+    convert_unit_classes(doc, units)
 
     print_warnings = verbose
 
@@ -109,6 +112,16 @@ def to_sbml(
     logger.info(f"OMEX archive written to {out}")
 
 
+def convert_unit_classes(doc: pe.EnzymeMLDocument, custom_units: list[UnitDefinition]):
+    custom_units.extend(
+        [
+            pe.UnitDefinition(**unit.model_dump())
+            for unit in _assign_ids_to_units(tools.find_unique(doc, pe.UnitDefinition))
+            if unit.id not in [unit.id for unit in custom_units]
+        ]
+    )
+
+
 def _add_unit_definitions(unit: UnitDefinition):
     """Add unit definitions to the SBML model."""
 

pyenzyme/tabular.py

@@ -59,7 +59,10 @@ def to_pandas(
         df["id"] = [meas.id] * len(df)
         dfs.append(df)
 
-    return pd.concat(dfs, ignore_index=True).reset_index(drop=True)
+    if dfs:
+        return pd.concat(dfs, ignore_index=True).reset_index(drop=True)
+    else:
+        return pd.DataFrame()
 
 
 def read_excel(