From e6ca959c39a2165e869c238a70b1ca223de0ee7b Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 26 Jun 2024 14:18:00 +0200 Subject: [PATCH] test --- .../benchmark-models/test_benchmark_collection.sh | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/tests/benchmark-models/test_benchmark_collection.sh b/tests/benchmark-models/test_benchmark_collection.sh index 6b9284f4e6..ec8432b723 100755 --- a/tests/benchmark-models/test_benchmark_collection.sh +++ b/tests/benchmark-models/test_benchmark_collection.sh @@ -89,7 +89,7 @@ for model in $models; do yaml="${model_dir}"/"${model}"/"${model}".yaml amici_model_dir=test_bmc/"${model}" mkdir -p "$amici_model_dir" - cmd_import="amici_import_petab -y ${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} @@ -111,3 +111,15 @@ for model in $models; do done cd "$script_path" && python evaluate_benchmark.py + +# Test deprecated import from individual PEtab files +model="Zheng_PNAS2012" +problem_dir="${model_dir}/${model}" +amici_model_dir=test_bmc/"${model}-deprecated" +mkdir -p "$amici_model_dir" +cmd_import="amici_import_petab -s "${problem_dir}/model_${model}.xml" \ + -m "${problem_dir}/measurementData_${model}.tsv" \ + -c "${problem_dir}/experimentalCondition_${model}.tsv" \ + -p "${problem_dir}/parameters_${model}.tsv" \ + -b "${problem_dir}/observables_${model}.tsv" \ + -o ${amici_model_dir} -n ${model} --no-compile"