Convert to PEtab v2

Author: dweindl

v1_v2.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+"""Convert benchmark problems from PEtab v1 to v2 format."""
+
+import logging
+import benchmark_models_petab
+from petab.v2.petab1to2 import petab1to2
+from pathlib import Path
+
+def main():
+    logging.basicConfig(level=logging.INFO)
+    v2_root = Path(__file__).resolve().parent / "v2"
+
+    for problem_id in benchmark_models_petab.MODELS:
+        convert(problem_id, output_dir=v2_root / problem_id)
+
+def convert(problem_id: str, output_dir: Path):
+    """Convert a PEtab v1 problem to v2 format."""
+    logging.info(f"Converting {problem_id}...")
+    yaml_path = benchmark_models_petab.get_problem_yaml_path(problem_id)
+    try:
+        petab1to2(yaml_path, output_dir)
+    except NotImplementedError as e:
+        logging.warning(f"Skipping {problem_id}: {e}")
+        return
+
+    logging.info(f"Converted {problem_id}.")
+
+
+if __name__ == "__main__":
+    main()