From 9359b247668c25a722b02e56b57aae1cc4cd5f7c Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 24 Oct 2024 11:09:05 +0200 Subject: [PATCH] .. --- .../benchmark-models/test_benchmark_collection.sh | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/tests/benchmark-models/test_benchmark_collection.sh b/tests/benchmark-models/test_benchmark_collection.sh index 581b8db028..d3d1cad712 100755 --- a/tests/benchmark-models/test_benchmark_collection.sh +++ b/tests/benchmark-models/test_benchmark_collection.sh @@ -93,9 +93,22 @@ for model in $models; do yaml="${model_dir}"/"${model}"/problem.yaml fi + # problems we need to flatten + to_flatten=( + "Bruno_JExpBot2016" "Chen_MSB2009" "Crauste_CellSystems2017" + "Fiedler_BMCSystBiol2016" "Fujita_SciSignal2010" "SalazarCavazos_MBoC2020" + ) + flatten="" + for item in "${to_flatten[@]}"; do + if [[ "$item" == "$model" ]]; then + flatten="--flatten" + break + fi + done + amici_model_dir=test_bmc/"${model}" mkdir -p "$amici_model_dir" - cmd_import="amici_import_petab ${yaml} -o ${amici_model_dir} -n ${model} --flatten" + cmd_import="amici_import_petab ${yaml} -o ${amici_model_dir} -n ${model} ${flatten}" cmd_run="$script_path/test_petab_model.py -y ${yaml} -d ${amici_model_dir} -m ${model} -c" printf '=%.0s' {1..40}