[Fix] Set depth to -1 when adding a Node via Pathway.add_node to be in sync with legacy_api (#408)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#408

epdb/models.py

@@ -2166,7 +2166,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         smiles: str,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        depth: Optional[int] = 0,
+        depth: Optional[int] = -1,
     ):
         return Node.create(self, smiles, depth, name=name, description=description)