Raise clear error for PEtab YAML missing problems section

`Problem.from_yaml` raised a raw `KeyError`/`IndexError` when the
`problems` list was missing or empty, instead of a helpful message.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: dweindl

petab/v1/problem.py

@@ -311,6 +311,10 @@ def get_path(filename):
         config = ProblemConfig(
             **yaml_config, base_path=base_path, filepath=filepath
         )
+        if not config.problems:
+            raise ValueError(
+                "The PEtab problem YAML file is missing a 'problems' section."
+            )
         problem0 = config.problems[0]
         # currently required for handling PEtab v2 in here
         problem0_ = yaml_config["problems"][0]

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:

tests/v1/test_petab.py

@@ -824,6 +824,18 @@ def test_problem_from_yaml_v1_empty():
     petab.Problem.from_yaml(yaml_config)
 
 
+def test_problem_from_yaml_v1_missing_problems():
+    """Test loading PEtab version 1 yaml without a `problems` section
+    raises a helpful error instead of a raw KeyError/IndexError"""
+    yaml_config = """
+    format_version: 1
+    parameter_file:
+    """
+    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