Metadata-Version: 1.1
Name: cobra
Version: 0.4.2b2
Summary: COBRApy is a package for constraints-based modeling of biological networks
Home-page: https://opencobra.github.io/cobrapy
Author: Daniel Robert Hyduke <danielhyduke@gmail.com>, Ali Ebrahim <aebrahim@ucsd.edu>
Author-email: aebrahim@ucsd.edu
License: LGPL/GPL v2+
Download-URL: https://pypi.python.org/pypi/cobra
Description: cobrapy
        =======
        
        |Build Status| |Coverage Status| |Build status| |PyPI|
        
        COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely
        used for genome-scale modeling of metabolic networks in both prokaryotes
        and eukaryotes. COBRApy is a constraint-based modeling package that is
        designed to accommodate the biological complexity of the next generation
        of COBRA models and provides access to commonly used COBRA methods, such
        as flux balance analysis, flux variability analysis, and gene deletion
        analyses.
        
        To install, please follow the `instructions <INSTALL.md>`__.
        
        The documentation is browseable online at
        `readthedocs <https://cobrapy.readthedocs.org/en/stable/>`__ and can
        also be
        `downloaded <https://readthedocs.org/projects/cobrapy/downloads/>`__.
        
        Please use the `Google
        Group <http://groups.google.com/group/cobra-pie>`__ for help. More
        information about opencobra is available at the
        `website <http://opencobra.github.io/>`__.
        
        If you use cobrapy in a scientific publication, please cite
        `doi:10.1186/1752-0509-7-74 <http://dx.doi.org/doi:10.1186/1752-0509-7-74>`__
        
        License
        -------
        
        The cobrapy 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) will be bound
        by its license 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 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.
        
        .. |Build Status| image:: https://travis-ci.org/opencobra/cobrapy.svg?branch=master
           :target: https://travis-ci.org/opencobra/cobrapy
        .. |Coverage Status| image:: https://coveralls.io/repos/opencobra/cobrapy/badge.svg?branch=master&service=github
           :target: https://coveralls.io/github/opencobra/cobrapy?branch=master
        .. |Build status| image:: https://ci.appveyor.com/api/projects/status/2o549lhjyukke8nd/branch/master?svg=true
           :target: https://ci.appveyor.com/project/aebrahim/cobrapy/branch/master
        .. |PyPI| image:: https://img.shields.io/pypi/v/cobra.svg
           :target: https://pypi.python.org/pypi/cobra
        
        
        Installation of cobrapy
        =======================
        
        For installation help, please use the `Google
        Group <http://groups.google.com/group/cobra-pie>`__. For usage
        instructions, please see the
        `documentation <https://cobrapy.readthedocs.org/en/latest/>`__.
        
        --------------
        
        All releases require Python 2.7+ or 3.4+ to be installed before
        proceeding. Mac OS X (10.7+) and Ubuntu ship with Python. Windows users
        without python can download and install python from the `python
        website <https://www.python.org/ftp/python/2.7.9/python-2.7.9.amd64.msi>`__.
        Please note that though Anaconda and other python distributions may work
        with cobrapy, they are not explicitly supported (yet!).
        
        Stable version installation
        ---------------------------
        
        cobrapy can be installed with any recent installation of pip.
        Instructions for several operating systems are below:
        
        Mac OS X or Linux
        ~~~~~~~~~~~~~~~~~
        
        0. `install
           pip <http://pip.readthedocs.org/en/latest/installing.html>`__.
        1. In a terminal, run ``sudo pip install cobra``
        
        Microsoft Windows
        ~~~~~~~~~~~~~~~~~
        
        The preferred installation method on Windows is also to use pip. The
        latest Windows installers for Python 2.7 and 3.4 include pip, so if you
        use those you will already have pip.
        
        1. In a terminal, run ``C:\Python27\Scripts\pip.exe install cobra`` (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/cobra/>`__.
        
        Hacking version installation
        ----------------------------
        
        Use pip to install `Cython <http://cython.org/>`__. Install libglpk
        using your package manger. This would be
        ``brew install homebrew/science/glpk`` on a Mac and
        ``sudo apt-get install libglpk-dev`` on debian-based systems (including
        Ubuntu and Mint). GLPK can also be compiled from the released source.
        
        Clone the git repository using your preferred mothod. Cloning from your
        own `github fork <https://help.github.com/articles/fork-a-repo>`__ is
        recommended! Afterwards, open a terminal, enter the cobrapy repository
        and run the following command:
        
        ::
        
            python setup.py develop --user
        
        Installation of optional dependencies
        =====================================
        
        Optional Dependencies
        ---------------------
        
        On windows, these can downloaded from [this site]
        (http://www.lfd.uci.edu/~gohlke/pythonlibs/). On Mac/Linux, they can be
        installed using pip, or from the OS package manager (e.g brew, apt,
        yum).
        
        1. `libsbml <http://sbml.org>`__ >= 5.10 to read/write SBML level 2
           files
        
           -  `Windows
              installer <http://www.lfd.uci.edu/~gohlke/pythonlibs/#libsbml>`__
           -  Use ``sudo pip install python-libsbml`` on Mac/Linux
        
        2. `lxml <http://lxml.de/>`__ to speed up read/write of SBML level 3
           files.
        3. `numpy <http://numpy.org>`__ >= 1.6.1 for double deletions
        
           -  `Windows
              installer <http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy>`__
        
        4. `scipy <http://scipy.org>`__ >= 0.11 for ArrayBasedModel and saving
           to \*.mat files.
        
           -  `Windows
              installer <http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy>`__
        
        Other solvers
        -------------
        
        cobrapy comes with bindings to the GNU Linear Programming Kit ([glpk]
        (http://www.gnu.org/software/glpk/)) using its own bindings called
        "cglpk" in cobrapy. In addition, cobrapy currently supports these linear
        programming solvers:
        
        -  ILOG/CPLEX (available with
           `Academic <https://www.ibm.com/developerworks/university/academicinitiative/>`__
           and
           `Commercial <http://www.ibm.com/software/integration/optimization/cplex-optimizer/>`__
           licenses).
        -  `gurobi <http://gurobi.com>`__
        -  `QSopt\_ex
           esolver <http://www.dii.uchile.cl/~daespino/ESolver_doc/main.html>`__
        -  `MOSEK <http://www.mosek.com/>`__
        -  `coin-or clp and cbc <http://coin-or.org/>`__ through
           `cylp <https://github.com/coin-or/CyLP>`__.
        
        ILOG/CPLEX, MOSEK, and Gurobi are commercial software packages that
        currently provide free licenses for academics and support both linear
        and quadratic programming. GLPK and clp are open source linear
        programming solvers; however, they may not be as robsut as the
        commercial solvers for mixed-integer and quadratic programming.
        QSopt\_ex esolver is also open source, and can solve linear programs
        using rational operations, giving exact solutions.
        
        Testing your installation
        =========================
        
        1. Start python
        2. Type the following into the Python shell
        
        .. code:: python
        
            from cobra.test import test_all
            test_all()
        
        You should see some skipped tests and expected failures, and the
        function should return ``False``.
        
Keywords: metabolism biology linear programming optimization flux balance analysis fba
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 :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
