diff --git a/tests/benchmark-models/test_benchmark_collection.sh b/tests/benchmark-models/test_benchmark_collection.sh index 4efd1c55bb..2cae1db484 100755 --- a/tests/benchmark-models/test_benchmark_collection.sh +++ b/tests/benchmark-models/test_benchmark_collection.sh @@ -2,8 +2,6 @@ # Import and run selected benchmark models with nominal parameters and check # agreement with reference values # -# Expects environment variable BENCHMARK_COLLECTION to provide path to -# benchmark collection model directory # Confirmed to be working models=" @@ -60,8 +58,6 @@ Zheng_PNAS2012" set -e -[[ -n "${BENCHMARK_COLLECTION}" ]] && model_dir="${BENCHMARK_COLLECTION}" - function show_help() { echo "-h: this help; -n: dry run, print commands; -b path_to_models_dir" } @@ -112,7 +108,7 @@ cd "$script_path" && python evaluate_benchmark.py # Test deprecated import from individual PEtab files model="Zheng_PNAS2012" -problem_dir="${model_dir}/${model}" +problem_dir=$(python3 -c "import benchmark_models_petab; print(str(benchmark_models_petab.get_problem_yaml_path('Zheng_PNAS2012').parent))") amici_model_dir=test_bmc/"${model}-deprecated" cmd_import="amici_import_petab -s "${problem_dir}/model_${model}.xml" \ -m "${problem_dir}/measurementData_${model}.tsv" \