From de446b61a05012ae8494b8c11efb6081cc4cc824 Mon Sep 17 00:00:00 2001
From: Jan Range <range.jan@web.de>
Date: Tue, 24 Sep 2024 12:22:28 +0200
Subject: [PATCH] fix units not recognized

---
 pyenzyme/sbml/serializer.py | 15 ++++++++++++++-
 pyenzyme/tabular.py         |  5 ++++-
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/pyenzyme/sbml/serializer.py b/pyenzyme/sbml/serializer.py
index de3e9b2..5e440eb 100644
--- a/pyenzyme/sbml/serializer.py
+++ b/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."""
 
diff --git a/pyenzyme/tabular.py b/pyenzyme/tabular.py
index 1185dd3..32c1e4e 100644
--- a/pyenzyme/tabular.py
+++ b/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(