Benchmarking-Initiative · dweindl · Jul 14, 2025 · Jul 22, 2025 · Jul 22, 2025 · Oct 16, 2025
@@ -0,0 +1,35 @@
+#!/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:
+        if problem_id == "Froehlich_CellSystems2018":
+            # naive conversion generates huge condition table
+            logging.warning("Skipping Froehlich_CellSystems2018 due to performance issues.")
+            continue
+
+        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()
@@ -0,0 +1,17 @@
+format_version: 2.0.0
+parameter_files:
+- parameters_Alkan_SciSignal2018.tsv
+model_files:
+  model_Alkan_SciSignal2018:
+    location: model_Alkan_SciSignal2018.xml
+    language: sbml
+measurement_files:
+- measurementData_Alkan_SciSignal2018.tsv
+condition_files:
+- experimentalCondition_Alkan_SciSignal2018.tsv
+experiment_files:
+- experiments.tsv
+observable_files:
+- observables_Alkan_SciSignal2018.tsv
+mapping_files: []
+extensions: {}
@@ -0,0 +1,220 @@
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@@ -0,0 +1,74 @@
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