Metadata-Version: 2.1
Name: masspy
Version: 0.1.0
Summary: MASSpy is a package for kinetic modeling and simulation of biological networks
Home-page: https://github.com/SBRG/masspy
Author: Zachary B. Haiman
Author-email: zhaiman@eng.ucsd.edu
Maintainer: Zachary B. Haiman
Maintainer-email: zhaiman@eng.ucsd.edu
License: LGPL/GPL v3+
Download-URL: https://pypi.python.org/pypi/masspy
Keywords: metabolism biology kinetic modeling simulation programmingcobra
Platform: GNU/Linux
Platform: Mac OS X >= 10.7
Platform: Microsoft Windows >= 7
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Requires-Dist: cobra (>=0.15.0)
Requires-Dist: depinfo
Requires-Dist: libroadrunner (>=1.5)
Requires-Dist: numpy (>=1.13.0)
Requires-Dist: pandas (>=0.17.0)
Requires-Dist: optlang (>=1.4.2)
Requires-Dist: scipy (>=1.2.0)
Requires-Dist: six (>=1.11.0)
Requires-Dist: sympy (>=1.0.0)
Requires-Dist: tabulate (>=0.8.1)
Requires-Dist: matplotlib (>=3.2.0)
Provides-Extra: all
Requires-Dist: escher ; extra == 'all'
Requires-Dist: simplejson ; extra == 'all'
Provides-Extra: escher
Requires-Dist: escher ; extra == 'escher'
Provides-Extra: json
Requires-Dist: simplejson ; extra == 'json'

MASSpy - Mass Action Stoichiometric Simulation in Python
========================================================

|PyPI|

What is MASSpy?
~~~~~~~~~~~~~~~
The **M**\ass **A**\ction **S**\toichiometric **S**\imulation **py**\thon
(**MASSpy**) package contains modules for the construction, simulation, and
analysis of kinetic models of biochemical reaction systems.

**MASSpy** is built to integrate seemlessly with **COBRApy**, a widely used
modeling software package for constraint-based reconstruction and analysis of
biochemical reaction systems. Therefore **MASSpy**  can be used seperately from
or in conjuction with **COBRApy**, thereby providing a wide range of modeling
workflows and techniques.

Additional information about **COBRApy** can be found in its
`documentation <https://cobrapy.readthedocs.io/en/latest/index.html>`_ or
`github page <https://github.com/opencobra/cobrapy>`_.

Cite
----
A manuscript is in preparation for publication and will be the proper reference
for citing the **MASSpy** in the future.

Installation
~~~~~~~~~~~~

The recommended method is to install **MASSpy** is to use ``pip`` to
`install masspy from PyPI <https://pypi.python.org/pypi/masspy>`_. It is
recommended to do this inside a `virtual environment
<http://docs.python-guide.org/en/latest/dev/virtualenvs/>`_)::

	pip install masspy

You can install all packages, including optional dependencies, directly by::

    pip install masspy[all]

If you downloaded the source code, run::

	pip install -e .

in the ``masspy`` source directory. For additional information, please refer to the
the `detailed installation instructions <INSTALL.rst>`_.

Contributing
~~~~~~~~~~~~

Contributions are always welcome! Please read the `contributions
guideline <.github/CONTRIBUTING.rst>`_
to get started.

License
-------

The **MASSpy** source is released under both the GPL and LGPL licenses. You
may choose which license you choose to use the software under. However,
please note that binary packages which include GLPK (such as the binary
wheels distributed at https://pypi.python.org/pypi/cobra) and
`libRoadRunner <https://pypi.org/project/libroadrunner/>`_ will be bound
by their licenses as well.

This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License or the Lesser GNU
General Public License as published by the Free Software Foundation,
either version 3 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.

.. |PyPI| image:: https://badge.fury.io/py/masspy.svg
    :target: https://pypi.python.org/pypi/masspy

Installation of MASSpy
=======================

All releases require Python 3.6+ to be installed before proceeding.
Users without python can download and install python from the `python website
<https://www.python.org/downloads/>`_.
Please note that though Anaconda and other python distributions may work
with **MASSpy**, they are not explicitly supported.

Stable version installation
~~~~~~~~~~~~~~~~~~~~~~~~~~~

**MASSpy** can be installed with any recent installation of pip.

You can install all packages, including optional dependencies, directly by::

    pip install masspy[all]

Instructions for several operating systems are below:

Mac OS X or Linux
-----------------

1. `install pip <http://pip.readthedocs.org/en/latest/installing.html>`_.
2. In a terminal, run ``sudo pip install masspy``

We highly recommend updating ``pip`` beforehand
(``pip install pip --upgrade``).

Microsoft Windows
-----------------

The preferred installation method on Windows is also to use pip. The
latest Windows installers for Python 3.4 and up include pip, so if you
use those you will already have pip.

1. In a terminal, run ``C:\Python36\Scripts\pip.exe install masspy``
(you may need to adjust the path accordingly).

To install without pip, you will need to download and use the
appropriate installer for your version of python from the `python
package index <https://pypi.python.org/pypi/masspy/>`_.

Installation for development
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Get the `detailed contribution instructions <CONTRIBUTING.rst>`_ for
contributing to **MASSpy**.

Testing your installation
=========================

Currently **MASSpy** is still under development and testing. We apologize
for the inconvenience and provide further details on this page in a
future update.

For now, if you have any questions or concerns, please email
zhaiman@eng.ucsd.edu with "masspy concerns" in the subject line and we will
get back to you as soon as we can.


