Metadata-Version: 2.1
Name: pypesto
Version: 0.2.3
Summary: python Parameter EStimation TOolbox
Home-page: https://github.com/icb-dcm/pypesto
Author: The pyPESTO developers
Author-email: yannik.schaelte@gmail.com
License: UNKNOWN
Description: # pyPESTO - Parameter EStimation TOolbox for python
        
        <img src="https://raw.githubusercontent.com/ICB-DCM/pyPESTO/master/doc/logo/logo_wordmark.png" width="50%" alt="pyPESTO logo"/>
        
        **pyPESTO** is a widely applicable and highly customizable toolbox for
        parameter estimation.
        
        [![PyPI](https://badge.fury.io/py/pypesto.svg)](https://badge.fury.io/py/pypesto)
        [![CI](https://github.com/ICB-DCM/pyPESTO/workflows/CI/badge.svg)](https://github.com/ICB-DCM/pyPESTO/actions)
        [![Coverage](https://codecov.io/gh/ICB-DCM/pyPESTO/branch/master/graph/badge.svg)](https://codecov.io/gh/ICB-DCM/pyPESTO)
        [![Quality](https://api.codacy.com/project/badge/Grade/134432ddad0e464b8494587ff370f661)](https://www.codacy.com/app/dweindl/pyPESTO?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=ICB-DCM/pyPESTO&amp;utm_campaign=Badge_Grade)
        [![Documentation](https://readthedocs.org/projects/pypesto/badge/?version=latest)](https://pypesto.readthedocs.io)
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2600850.svg)](https://zenodo.org/record/2600850#.XVuwkHduJfF)
        
        ## Feature overview
        
        pyPESTO features include:
        
        * Multi-start local optimization
        * Profile computation
        * Result visualization
        * Interface to [AMICI](https://github.com/ICB-DCM/AMICI/) for efficient
          simulation and sensitivity analysis of ordinary differential equation (ODE)
          models
          ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/boehm_JProteomeRes2014.ipynb))
        * Parameter estimation pipeline for systems biology problems specified in
          [SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
          ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/petab_import.ipynb))
        * Parameter estimation with qualitative data as described in
          [Schmiester et al. (2019)](https://www.biorxiv.org/content/10.1101/848648v1).
          This is currently implemented in the `feature_ordinal` branch.
        
        ## Quick install
        
        The simplest way to install **pyPESTO** is via pip:
        
        ```shell
        pip3 install pypesto
        ```
        
        More information is available here:
        https://pypesto.readthedocs.io/en/latest/install.html
        
        ## Documentation
        
        The documentation is hosted on readthedocs.io:
        <https://pypesto.readthedocs.io>
        
        ## Examples
        
        Multiple use cases are discussed in the documentation. In particular, there are
        jupyter notebooks in the [doc/example](doc/example) directory.
        
        ## Contributing
        
        We are happy about any contributions. For more information on how to contribute
        to pyPESTO check out
        <https://pypesto.readthedocs.io/en/latest/contribute.html>
        
        ## References
        
        [**PESTO**](https://github.com/ICB-DCM/PESTO/):
        Parameter estimation toolbox for MATLAB. Development is discontinued, but PESTO
        comes with additional features waiting to be ported to pyPESTO.
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: amici
Provides-Extra: petab
Provides-Extra: ipopt
Provides-Extra: dlib
Provides-Extra: nlopt
Provides-Extra: pyswarm
Provides-Extra: cmaes
Provides-Extra: fides
Provides-Extra: pymc3
Provides-Extra: test
Provides-Extra: docs
Provides-Extra: quality
