From 432dac47e0bd26707e2043ea62821d6e19ade711 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 2 Oct 2025 10:49:51 +0200
Subject: [PATCH] doc: petab1to2

Closes #388.
---
 petab/v2/petab1to2.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/petab/v2/petab1to2.py b/petab/v2/petab1to2.py
index 5e5c5ae7..8e1c7e85 100644
--- a/petab/v2/petab1to2.py
+++ b/petab/v2/petab1to2.py
@@ -30,6 +30,17 @@ def petab1to2(
 
     Convert a PEtab problem from PEtab 1.0 to PEtab 2.0 format.
 
+    .. note::
+
+       Some aspects of PEtab v1 were not well-defined. For example, model
+       initialization order (e.g., applying initial assignments before or
+       after condition table overrides) and the impact of compartment size
+       changes were not specified. In such cases, we made assumptions that are
+       consistent with the clarified PEtab v2 specifications,
+       the PEtab test suite, or common practice.
+       Therefore, it is recommended to carefully review the generated PEtab v2
+       problem to ensure it aligns with the expected behavior.
+
     :param yaml_config:
         The PEtab problem as dictionary or YAML file name.
     :param output_dir: