petabtests 0.0.0a2

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 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

Evaluate results

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.

-> Overview of passed test cases for different tools supporting PEtab