Metadata-Version: 2.1
Name: petabtests
Version: 0.0.0a6
Summary: PEtab testsuite library
Home-page: https://github.com/PEtab-dev/petab_test_suite
Author: PEtab-dev
Author-email: yannik.schaelte@gmail.com
Maintainer: PEtab-dev
Maintainer-email: yannik.schaelte@gmail.com
License: UNKNOWN
Description: # PEtab test suite
        
        The PEtab test suite is a collection of test models for the
        [PEtab](https://github.com/petab-dev/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](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](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](petabtests/evaluate.py).
        
        -> [Overview of passed test cases for different tools supporting PEtab](https://github.com/PEtab-dev/PEtab#petab-features-supported-in-different-tools)
        
Keywords: PEtab testsuite
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
