PEtab testsuite library
PEtab test suite
The PEtab test suite is a collection of test models for the PEtab parameter estimation data format. It is intended to be used to verify and quantify PEtab-support by developers of tools for model simulation and parameter estimation.
Download and install the test suite
The PEtab test suite can be downloaded from GitHub via
git clone https://github.com/petab-dev/petab_test_suite
The test suite comes with all necessary files pregenerated. In the petabtests subdirectory, it contains a python module for generating the tests and evaluating results. This can be installed via
cd petab_test_suite pip3 install -e .
Use the test suite
The cases subdirectory contains a collection of enumerated tests.
Each test contains a descriptive
wxyz.md file, and a script file
file that can be used to generate all problem and solution files for the test.
The necessary files are in the same case specific folder, starting with an
In each case folder, there is a file
_wxyz.yaml containing the parameter
estimation problem description, and a file
information on the expected results: chi2 value, log-likelihood, simulation
table reference, and tolerances.
After download, all necessary files are already pregenerated.
Further, installation of the petabtests module installs a routine to recreate the problem and solution files for all test problems. It can be invoked via
cd petab_test_suite petabtests_create
To evaluate how a tool performs on a given test problem, three metrics are employed: Simulations, chi2 value and log-likelihood. A tool can be said to cover a test problem if any of those values matches the ground truth values up to some tolerance.
The python module provides convenience functions for evaluation in petabtests/evaluate.py.
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