From cb32d940159aadf8590574bb483c4e5ebb2f084e Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Tue, 22 Jul 2025 12:28:50 +0200
Subject: [PATCH] v1v2-converter: handle log10-normal

PEtab v2 does not support log10-type distributions. When upconverting PEtab v1 problems, replace log10-normal by log-normal and emit a warning.
---
 petab/v2/petab1to2.py       | 11 +++++++++++
 tests/v2/test_conversion.py |  3 +++
 2 files changed, 14 insertions(+)

diff --git a/petab/v2/petab1to2.py b/petab/v2/petab1to2.py
index 4b040df7..5e5c5ae7 100644
--- a/petab/v2/petab1to2.py
+++ b/petab/v2/petab1to2.py
@@ -4,6 +4,7 @@
 
 import re
 import shutil
+import warnings
 from contextlib import suppress
 from pathlib import Path
 from tempfile import TemporaryDirectory
@@ -386,6 +387,16 @@ def update_noise_dist(row):
             else:
                 new_dist = f"{trans}-{dist}"
 
+            if new_dist == "log10-normal":
+                warnings.warn(
+                    f"Noise distribution `{new_dist}' for "
+                    f"observable `{row[v1.C.OBSERVABLE_ID]}'"
+                    f" is not supported in PEtab v2. "
+                    "Using `log-normal` instead.",
+                    stacklevel=2,
+                )
+                new_dist = v2.C.LOG_NORMAL
+
             if new_dist not in v2.C.NOISE_DISTRIBUTIONS:
                 raise NotImplementedError(
                     f"Noise distribution `{new_dist}' for "
diff --git a/tests/v2/test_conversion.py b/tests/v2/test_conversion.py
index 6bcbb22c..eb8f9d45 100644
--- a/tests/v2/test_conversion.py
+++ b/tests/v2/test_conversion.py
@@ -30,6 +30,9 @@ def test_petab1to2_remote():
     )
 
 
+@pytest.mark.filterwarnings(
+    "ignore:.*Using `log-normal` instead.*:UserWarning"
+)
 @parametrize_or_skip
 def test_benchmark_collection(problem_id):
     """Test that we can upgrade all benchmark collection models."""