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.
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 .
The cases subdirectory contains a collection of enumerated tests.
Each test contains a descriptive wxyz.md file, and a script file wxyz.py
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
underscore.
In each case folder, there is a file _wxyz.yaml containing the parameter
estimation problem description, and a file _wxyz_solution.yaml containing
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.
TODO A table with cases as rows will be created, with a column for each tool, indicating whether the test case is covered. Additional information if the tool allows to compute e.g. likelihood, or only chi2 values, is supposed to be provided.