Metadata-Version: 2.1
Name: cobra
Version: 0.14.1
Summary: COBRApy is a package for constraints-based modeling of biological networks
Home-page: https://opencobra.github.io/cobrapy
Author: The cobrapy core team
Author-email: cobra-pie@googlegroups.com
Maintainer: Moritz E. Beber
Maintainer-email: morbeb@biosustain.dtu.dk
License: LGPL/GPL v2+
Download-URL: https://pypi.python.org/pypi/cobra
Description: cobrapy - Constraint-Based Reconstruction and Analysis in Python
        ================================================================
        
        |Build Status| |Coverage Status| |Build status| |PyPI| |Gitter|
        
        What is cobrapy?
        ~~~~~~~~~~~~~~~~
        
        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.
        
        Our aim with cobrapy is to provide useful, efficient infrastructure
        for:
        
        - creating and managing metabolic models
        - accessing popular solvers
        - analyzing models with methods such as FVA, FBA, pFBA, MOMA etc.
        - inspecting models and drawing conclusions on gene essentiality,
          testing consequences of knock-outs etc.
        
        Our goal with cobrapy is for it to be useful on its own, and for it to
        be the natural choice of infrastructure for developers that want to
        build new COBRA related python packages for e.g. visualization,
        strain-design and data driven analysis. By re-using the same classes
        and design principles, we can make new methods both easier to
        implement and easier to use, thereby bringing the power of COBRA to
        more researchers.
        
        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. By writing a well formulated question, with sufficient
        detail, you are much more likely to quickly receive a good answer! Please refer to these `StackOverflow
        guidelines <https://stackoverflow.com/help/how-to-ask>`_ on how to ask questions.
        Alternatively, you can use `gitter.im <https://gitter.im/opencobra/cobrapy>`_ for quick questions
        and discussions about cobrapy (faster response times). Please keep in mind that answers are provided on a volunteer
        basis.
        
        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>`_
        
        Installation
        ~~~~~~~~~~~~
        
        Use pip to `install cobrapy from
        PyPI <https://pypi.python.org/pypi/cobra>`_ (we recommend doing this
        inside a `virtual
        environment <http://docs.python-guide.org/en/latest/dev/virtualenvs/>`_)::
        
            pip install cobra
        
        In case you downloaded the source code, run::
        
            pip install -e .
        
        In the ``cobrapy`` directory. For further information, please follow
        the `detailed installation instructions <INSTALL.rst>`_.
        
        Contributing
        ~~~~~~~~~~~~
        
        Contributions are always welcome! Please read the `contributions
        guideline <.github/CONTRIBUTING.rst>`_ to get started.
        
        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://codecov.io/github/opencobra/cobrapy/coverage.svg?branch=master
           :target: https://codecov.io/github/opencobra/cobrapy
        .. |Build status| image:: https://ci.appveyor.com/api/projects/status/qmqdy67jbwbc3ds7/branch/master?svg=true
           :target: https://ci.appveyor.com/project/cobrapy39491/cobrapy/branch/master
        .. |PyPI| image:: https://badge.fury.io/py/cobra.svg
           :target: https://pypi.python.org/pypi/cobra
        .. |Gitter| image:: https://badges.gitter.im/opencobra/cobrapy.svg
           :target: https://gitter.im/opencobra/cobrapy?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge
        
        
        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
        -----------------
        
        1. `install
           pip <http://pip.readthedocs.org/en/latest/installing.html>`_.
        2. In a terminal, run ``sudo pip install cobra``
        
        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 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/>`_.
        
        Installation for development
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Get the `detailed contribution instructions <CONTRIBUTING.rst>`_ for contributing to cobrapy.
        
        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 libsbml 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. `scipy <http://scipy.org>`_ >= 0.11 for MOMA and saving to \*.mat files.
           -  `Windows scipy installer <http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy>`_
        
        4. `pytest <http://docs.pytest.org/en/latest/>`_ and `pytest-benchmark
           <http://pytest-benchmark.readthedocs.io/en/latest/>`_ are required
           for testing
        
        You can install all packages directly by
        
        .. code:: shell
        
            pip install "cobra[all]"
        
        Solvers
        ~~~~~~~~~~~~~
        
        cobrapy uses `optlang <http://optlang.readthedocs.io>`_ to interface
        the mathematical solvers used to optimize the created COBRA models,
        which at the time of writing
        
        -  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>`_
        -  `glpk <http://www.gnu.org/software/glpk/>`_
        
        Testing your installation
        =========================
        
        While it is not a hard requirement for using cobrapy, you need pytest and
        pytest-benchmark to run its tests. First do
        
        .. code:: shell
        
            pip install pytest pytest-benchmark
        
        or to install cobrapy directly with the test dependencies
        
        .. code:: shell
        
           pip install "cobra[test]"
        
        Then start python and 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 ``0``. If you see a value other than ``0`` please file
        an `issue report <CONTRIBUTING.rst>`_.
        
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 :: 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
Provides-Extra: sbml
Provides-Extra: array
Provides-Extra: all
