From 764b2be7af807589004e9bc008c65e45777009d6 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Tue, 22 Sep 2026 16:45:32 +0200
Subject: [PATCH] Raise clear error for PEtab YAML with empty `problems`
 section

`Problem.from_yaml` raised a raw `KeyError`/`IndexError` when the
`problems` list was empty or absent (which pydantic silently defaults
to an empty list), instead of a helpful message.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
---
 petab/v1/problem.py    |  5 +++++
 petab/v1/yaml.py       |  2 +-
 tests/v1/test_petab.py | 23 +++++++++++++++++++++++
 3 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/petab/v1/problem.py b/petab/v1/problem.py
index ae09e75b..96401f9b 100644
--- a/petab/v1/problem.py
+++ b/petab/v1/problem.py
@@ -311,6 +311,11 @@ def get_path(filename):
         config = ProblemConfig(
             **yaml_config, base_path=base_path, filepath=filepath
         )
+        if not config.problems:
+            raise ValueError(
+                "The 'problems' section of the PEtab problem YAML file "
+                "must not be empty."
+            )
         problem0 = config.problems[0]
         # currently required for handling PEtab v2 in here
         problem0_ = yaml_config["problems"][0]
diff --git a/petab/v1/yaml.py b/petab/v1/yaml.py
index 669c192f..0167934f 100644
--- a/petab/v1/yaml.py
+++ b/petab/v1/yaml.py
@@ -205,7 +205,7 @@ def is_composite_problem(yaml_config: dict | str | Path) -> bool:
         yaml_config: PEtab configuration as dictionary or YAML file name
     """
     yaml_config = load_yaml(yaml_config)
-    return len(yaml_config[PROBLEMS]) > 1
+    return len(yaml_config.get(PROBLEMS, [])) > 1
 
 
 def assert_single_condition_and_sbml_file(problem_config: dict) -> None:
diff --git a/tests/v1/test_petab.py b/tests/v1/test_petab.py
index fd882205..b7e36123 100644
--- a/tests/v1/test_petab.py
+++ b/tests/v1/test_petab.py
@@ -824,6 +824,29 @@ def test_problem_from_yaml_v1_empty():
     petab.Problem.from_yaml(yaml_config)
 
 
+@pytest.mark.parametrize(
+    "yaml_config",
+    [
+        """
+        format_version: 1
+        parameter_file:
+        """,
+        """
+        format_version: 1
+        parameter_file:
+        problems: []
+        """,
+    ],
+)
+def test_problem_from_yaml_v1_empty_problems(yaml_config):
+    """Test loading PEtab version 1 yaml with a missing or empty
+    `problems` section raises a helpful error instead of a raw
+    KeyError/IndexError"""
+    yaml_config = safe_load(StringIO(yaml_config))
+    with pytest.raises(ValueError, match="problems"):
+        petab.Problem.from_yaml(yaml_config)
+
+
 def test_problem_from_yaml_v1_multiple_files():
     """Test loading PEtab version 1 yaml with multiple condition / measurement
     / observable files