Metadata-Version: 2.1
Name: pyabc
Version: 0.11.9
Summary: Distributed, likelihood-free ABC-SMC inference
Home-page: https://github.com/icb-dcm/pyabc
Author: The pyABC developers
Author-email: yannik.schaelte@gmail.com
Maintainer: Yannik Schaelte
Maintainer-email: yannik.schaelte@gmail.com
License: BSD-3-Clause
Download-URL: https://github.com/icb-dcm/pyabc/releases
Project-URL: Bug Tracker, https://github.com/icb-dcm/pyabc/issues
Project-URL: Documentation, https://pyabc.readthedocs.io
Project-URL: Changelog, https://pyabc.readthedocs.io/en/latest/releasenotes.html
Keywords: likelihood-free,inference,abc,approximate bayesian computation,sge,distributed
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Requires-Dist: numpy (>=1.19.1)
Requires-Dist: scipy (>=1.5.2)
Requires-Dist: pandas (>=1.2.0)
Requires-Dist: cloudpickle (>=1.5.0)
Requires-Dist: scikit-learn (>=0.23.1)
Requires-Dist: click (>=7.1.2)
Requires-Dist: redis (>=2.10.6)
Requires-Dist: distributed (>=2021.10.0)
Requires-Dist: matplotlib (>=3.3.0)
Requires-Dist: sqlalchemy (>=1.3.18)
Requires-Dist: jabbar (>=0.0.10)
Requires-Dist: gitpython (>=3.1.7)
Provides-Extra: r
Requires-Dist: rpy2 (>=3.4.4) ; extra == 'r'
Requires-Dist: cffi (>=1.14.5) ; extra == 'r'
Requires-Dist: ipython (>=7.18.1) ; extra == 'r'
Requires-Dist: pygments (>=2.6.1) ; extra == 'r'
Provides-Extra: amici
Requires-Dist: amici (>=0.11.19) ; extra == 'amici'
Provides-Extra: doc
Requires-Dist: sphinx (>=3.1.0) ; extra == 'doc'
Requires-Dist: nbsphinx (>=0.7.0) ; extra == 'doc'
Requires-Dist: nbconvert (>=5.6.1) ; extra == 'doc'
Requires-Dist: sphinx-rtd-theme (>=0.4.3) ; extra == 'doc'
Requires-Dist: sphinx-autodoc-typehints (>=1.11.1) ; extra == 'doc'
Requires-Dist: ipython (>=7.18.1) ; extra == 'doc'
Provides-Extra: examples
Requires-Dist: notebook (>=6.1.4) ; extra == 'examples'
Provides-Extra: julia
Requires-Dist: julia (>=0.5.7) ; extra == 'julia'
Requires-Dist: pygments (>=2.6.1) ; extra == 'julia'
Provides-Extra: migrate
Requires-Dist: alembic (>=1.5.4) ; extra == 'migrate'
Provides-Extra: ot
Requires-Dist: pot (>=0.7.0) ; extra == 'ot'
Provides-Extra: petab
Requires-Dist: petab (>=0.1.18) ; extra == 'petab'
Provides-Extra: plotly
Requires-Dist: plotly (>=5.3.1) ; extra == 'plotly'
Requires-Dist: kaleido (>=0.2.1) ; extra == 'plotly'
Provides-Extra: pyarrow
Requires-Dist: pyarrow (>=6.0.0) ; extra == 'pyarrow'
Provides-Extra: test
Requires-Dist: pytest (>=5.4.3) ; extra == 'test'
Requires-Dist: pytest-cov (>=2.10.0) ; extra == 'test'
Requires-Dist: pytest-rerunfailures (>=9.1.1) ; extra == 'test'
Provides-Extra: test_petab
Requires-Dist: petabtests (>=0.0.0a6) ; extra == 'test_petab'
Provides-Extra: webserver
Requires-Dist: flask-bootstrap (>=3.3.7.1) ; extra == 'webserver'
Requires-Dist: flask (>=1.1.2) ; extra == 'webserver'
Requires-Dist: bokeh (>=2.1.1) ; extra == 'webserver'
Provides-Extra: yaml2sbml
Requires-Dist: yaml2sbml (>=0.2.1) ; extra == 'yaml2sbml'

pyABC
=====

.. figure:: https://raw.githubusercontent.com/ICB-DCM/pyABC/main/doc/logo/logo.svg
   :alt: pyABC logo
   :width: 30 %
   :align: center

|CI| |docs| |codecov| |pypi| |doi| |black|

Massively parallel, distributed and scalable ABC-SMC
(Approximate Bayesian Computation - Sequential Monte Carlo)
for parameter estimation of complex stochastic models.
Implemented in Python with support of the R language.

- **Documentation:** `https://pyabc.readthedocs.io <https://pyabc.readthedocs.io>`_
- **Contact:** `https://pyabc.readthedocs.io/en/latest/about.html <https://pyabc.readthedocs.io/en/latest/about.html>`_
- **Source:** `https://github.com/icb-dcm/pyabc <https://github.com/icb-dcm/pyabc>`_
- **Bug reports:** `https://github.com/icb-dcm/pyabc/issues <https://github.com/icb-dcm/pyabc/issues>`_

Examples
--------

Many examples are available as Jupyter Notebooks in the
`examples directory <https://github.com/icb-dcm/pyabc/tree/main/doc/examples>`_
and also for download and for online inspection in the
`example section of the documentation <http://pyabc.readthedocs.io/en/latest/examples.html>`_.


.. |CI| image:: https://github.com/ICB-DCM/pyABC/workflows/CI/badge.svg
   :target: https://github.com/ICB-DCM/pyABC/actions
   :alt: CI

.. |docs| image:: https://readthedocs.org/projects/pyabc/badge/?version=latest
   :target: http://pyabc.readthedocs.io/en/latest/
   :alt: Docs

.. |codecov| image:: https://codecov.io/gh/ICB-DCM/pyABC/branch/main/graph/badge.svg
   :target: https://codecov.io/gh/ICB-DCM/pyABC
   :alt: Codecov

.. |pypi| image:: https://badge.fury.io/py/pyabc.svg
   :target: https://badge.fury.io/py/pyabc
   :alt: PyPI

.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3257587.svg
   :target: https://doi.org/10.5281/zenodo.3257587
   :alt: DOI

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/psf/black
   :alt: Code style: Black


