Metadata-Version: 2.1
Name: sbmlsim
Version: 0.1.9
Summary: sbmlsim are utilities for simulation of SBML.
Home-page: https://github.com/matthiaskoenig/sbmlsim
Author: Matthias Koenig
Author-email: konigmatt@googlemail.com
Maintainer: Matthias Koenig
Maintainer-email: konigmatt@googlemail.com
License: LGPL-3.0
Download-URL: https://pypi.org/project/sbmlsim
Project-URL: Source Code, https://github.com/matthiaskoenig/sbmlsim
Project-URL: Documentation, https://sbmlsim.readthedocs.io
Project-URL: Bug Tracker, https://github.com/matthiaskoenig/sbmlsim/issues
Keywords: modeling,standardization,SBML
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/x-rst
Requires-Dist: numpy (>=1.19.2)
Requires-Dist: scipy (>=1.5.1)
Requires-Dist: sympy (>=1.6.1)
Requires-Dist: pandas (>=1.1.3)
Requires-Dist: tables (>=3.6.1)
Requires-Dist: xarray (>=0.15.1)
Requires-Dist: bottleneck (>=1.3.2)
Requires-Dist: pint (>=0.16.1)
Requires-Dist: python-libsbml-experimental (>=5.18.1)
Requires-Dist: python-libsedml (>=2.0.11)
Requires-Dist: python-libcombine (>=0.2.7)
Requires-Dist: python-libnuml (>=1.1.1)
Requires-Dist: libroadrunner (>=2.0.0)
Requires-Dist: psutil (>=5.6.3)
Requires-Dist: setproctitle (>=1.1.10)
Requires-Dist: matplotlib (>=3.3.0)
Requires-Dist: plotly
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Provides-Extra: development
Requires-Dist: black ; extra == 'development'
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Requires-Dist: tox ; extra == 'development'
Requires-Dist: pytest (>=6.1) ; extra == 'development'
Requires-Dist: pytest-cov (>=2.8.1) ; extra == 'development'

sbmlsim: SBML simulation made easy
==================================

.. image:: https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg
   :target: https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD
   :alt: GitHub Actions CI/CD Status

.. image:: https://img.shields.io/pypi/v/sbmlsim.svg
   :target: https://pypi.org/project/sbmlsim/
   :alt: Current PyPI Version

.. image:: https://img.shields.io/pypi/pyversions/sbmlsim.svg
   :target: https://pypi.org/project/sbmlsim/
   :alt: Supported Python Versions

.. image:: https://img.shields.io/pypi/l/sbmlsim.svg
   :target: http://opensource.org/licenses/LGPL-3.0
   :alt: GNU Lesser General Public License 3

.. image:: https://codecov.io/gh/matthiaskoenig/sbmlsim/branch/develop/graph/badge.svg
   :target: https://codecov.io/gh/matthiaskoenig/sbmlsim
   :alt: Codecov

.. image:: https://readthedocs.org/projects/sbmlsim/badge/?version=latest
   :target: https://sbmlsim.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg
   :target: https://doi.org/10.5281/zenodo.3597770
   :alt: Zenodo DOI

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


sbmlsim is a collection of python utilities to simulate to simplify simulations with
`SBML <http://www.sbml.org>`__ models implemented on top of
`roadrunner <http://libroadrunner.org/>`__. Source code is available from
`https://github.com/matthiaskoenig/sbmlsim <https://github.com/matthiaskoenig/sbmlsim>`__.

Features include among others

-  simulation experiments
-  simulation reports
-  parameter fitting

The documentation is available on `https://sbmlsim.readthedocs.io <https://sbmlsim.readthedocs.io>`__.
If you have any questions or issues please `open an issue <https://github.com/matthiaskoenig/sbmlsim/issues>`__.


How to cite
===========
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3597770.svg
   :target: https://doi.org/10.5281/zenodo.3597770
   :alt: Zenodo DOI

License
=======

* Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__
* Documentation: `CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__

The sbmlsim source is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License or the GNU Lesser General Public
License as published by the Free Software Foundation, either version 2 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding
=======
Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054).

Installation
============
``sbmlsim`` is available from `pypi <https://pypi.python.org/pypi/sbmlsim>`__ and
can be installed via::

    pip install sbmlsim

Requirements
------------

HDF5 support is required which can be installed on linux via::

    sudo apt-get install -y libhdf5-serial-dev

Develop version
---------------
The latest develop version can be installed via::

    pip install git+https://github.com/matthiaskoenig/sbmlsim.git@develop

Or via cloning the repository and installing via::

    git clone https://github.com/matthiaskoenig/sbmlsim.git
    cd sbmlsim
    pip install -e .

To install for development use::

    pip install -e .[development]

© 2019-2020 Matthias König


