v1v2-converter: handle log10-normal (PEtab-dev#413)

PEtab v2 does not support log10-type distributions. When upconverting PEtab v1 problems, replace log10-normal by log-normal and emit a warning.

Author: dweindl

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 "

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."""