Metadata-Version: 1.1
Name: scikit-bio
Version: 0.1.5
Summary: Data structures, algorithms and educational resources for bioinformatics.
Home-page: http://scikit-bio.org
Author: scikit-bio development team
Author-email: gregcaporaso@gmail.com
License: BSD
Description: ::
        
                       _ _    _ _          _     _
                      (_) |  (_) |        | |   (_)
              ___  ___ _| | ___| |_ ______| |__  _  ___
             / __|/ __| | |/ / | __|______| '_ \| |/ _ \
             \__ \ (__| |   <| | |_       | |_) | | (_) |
             |___/\___|_|_|\_\_|\__|      |_.__/|_|\___/
        
        
                   Opisthokonta
                           \  Amoebozoa
                            \ /
                             *    Euryarchaeota
                              \     |_ Crenarchaeota
                               \   *
                                \ /
                                 *
                                /
                               /
                              /
                             *
                            / \
                           /   \
                Proteobacteria  \
                               Cyanobacteria
        
        |Build Status| |Coverage Status|
        
        scikit-bio is an open-source, BSD-licensed python package providing data structures, algorithms and educational resources for bioinformatics.
        
        scikit-bio is currently in pre-alpha release stage. We are very actively developing it, and **backwards-incompatible interface changes can and will arise**. Once the API has started to solidify, we will strive to maintain backwards compatibility. We will provide deprecation warnings, etc. wherever possible.
        
        To view scikit-bio's documentation, visit `scikit-bio.org
        <http://scikit-bio.org>`__.
        
        Installation of release version (recommended for most users)
        ------------------------------------------------------------
        
        To install the latest release version of scikit-bio you should run::
        
            pip install numpy
            pip install scikit-bio
        
        If you'd like to install the dependencies manually (or some other way
        than using pip), you can find those here:
        
        -  `Python <http://www.python.org/>`__ 2.7 or >= 3.3
        -  `numpy <http://www.numpy.org/>`__ >= 1.7
        -  `scipy <http://www.scipy.org/>`__ >= 0.13.0
        -  `matplotlib <http://www.matplotlib.org/>`__ >= 1.1.0
        -  `pandas <http://pandas.pydata.org/>`__
        -  `future <https://pypi.python.org/pypi/future>`__
        -  `natsort <https://pypi.python.org/pypi/natsort>`__
        
        If you have trouble getting these dependencies installed (scipy, in particular, can be tricky), you should try installing `Canopy Express <https://www.enthought.com/canopy-express/>`_, which includes all of these dependencies. You should then be able to easily install scikit-bio by running::
        
            pip install scikit-bio
        
        After installation with ``pip``, you can run the scikit-bio unittest suite as follows::
        
            nosetests --with-doctest skbio
        
        Installation of development version
        -----------------------------------
        
        If you're interested in working with the latest development release of scikit-bio (recommended for developers only, as the development code can be unstable and less documented than the release code), you can clone the repository and install as follows. This will require that you have ``git`` installed.
        ::
        
            git clone git@github.com:biocore/scikit-bio.git
            cd scikit-bio
            pip install .
        
        After this completes, you can run the scikit-bio unittest suite as follows. You must first ``cd`` out of the ``scikit-bio`` directory for the tests to pass (here we ``cd`` to the home directory).
        ::
        
            cd
            nosetests --with-doctest skbio
        
        For developers of scikit-bio, if you don't want to be forced to re-install after every change, you can modify the above ``pip install`` command to::
        
            pip install -e .
        
        This will build scikit-bio's cython extensions, and will create a link in the ``site-packages`` directory to the scikit-bio source directory. When you then make changes to code in the source directory, those will be used (e.g., by the unittests) without re-installing.
        
        Finally, if you don't want to use ``pip`` to install scikit-bio, and prefer to just put ``scikit-bio`` in your ``$PYTHONPATH``, at the minimum you should run::
        
            python setup.py build_ext --inplace
        
        This will build scikit-bio's cython extensions, but not create a link to the scikit-bio source directory in ``site-packages``. If this isn't done, using certain components of scikit-bio will be inefficient and will produce an ``EfficiencyWarning``.
        
        Getting help
        ------------
        
        To get help with scikit-bio, you should use the `skbio <http://stackoverflow.com/questions/tagged/skbio>`_ tag on StackOverflow (SO). Before posting a question, check out SO's guide on how to `ask a question <http://stackoverflow.com/questions/how-to-ask>`_. The scikit-bio developers regularly monitor the skbio SO tag.
        
        Licensing
        ---------
        
        scikit-bio is available under the new BSD license. See
        `COPYING.txt <https://github.com/biocore/scikit-bio/blob/master/COPYING.txt>`__ for scikit-bio's license, and the
        `licenses directory <https://github.com/biocore/scikit-bio/tree/master/licenses>`_ for the licenses of third-party software that is
        (either partially or entirely) distributed with scikit-bio.
        
        Projects using scikit-bio
        -------------------------
        
        Some of the projects that we know of that are using scikit-bio are:
        
        -  `QIIME <http://qiime.org/>`__
        -  `Emperor <http://biocore.github.io/emperor/>`__
        -  `An Introduction to Applied
           Bioinformatics <http://caporasolab.us/An-Introduction-To-Applied-Bioinformatics/>`__
        -  `tax2tree <https://github.com/biocore/tax2tree>`__
        
        If you're using scikit-bio in your own projects, you can issue a
        pull request to add them to this list.
        
        scikit-bio development
        ----------------------
        
        If you're interested in getting involved in or learning about
        scikit-bio development, see `CONTRIBUTING.md <https://github.com/biocore/scikit-bio/blob/master/CONTRIBUTING.md>`__.
        
        See the `list of all of scikit-bio's contributors
        <https://github.com/biocore/scikit-bio/graphs/contributors>`__.
        
        Summaries of our weekly developer meetings are posted on
        HackPad. Click `here
        <https://hackpad.com/2014-scikit-bio-developer-meeting-notes-1S2RbMqy0iM>`__
        to view the meeting notes for 2014.
        
        The pre-history of scikit-bio
        -----------------------------
        
        scikit-bio began from code derived from `PyCogent
        <http://www.pycogent.org>`__ and `QIIME <http://www.qiime.org>`__, and
        the contributors and/or copyright holders have agreed to make the code
        they wrote for PyCogent and/or QIIME available under the BSD
        license. The contributors to PyCogent and/or QIIME modules that have
        been ported to scikit-bio are: Rob Knight (`@rob-knight
        <https://github.com/rob-knight>`__), Gavin Huttley (`@gavin-huttley
        <https://github.com/gavin-huttley>`__), Daniel McDonald (`@wasade
        <https://github.com/wasade>`__), Micah Hamady, Antonio Gonzalez
        (`@antgonza <https://github.com/antgonza>`__), Sandra Smit, Greg
        Caporaso (`@gregcaporaso <https://github.com/gregcaporaso>`__), Jai
        Ram Rideout (`@ElBrogrammer <https://github.com/ElBrogrammer>`__),
        Cathy Lozupone (`@clozupone <https://github.com/clozupone>`__), Mike Robeson
        (`@mikerobeson <https://github.com/mikerobeson>`__), Marcin Cieslik,
        Peter Maxwell, Jeremy Widmann, Zongzhi Liu, Michael Dwan, Logan Knecht
        (`@loganknecht <https://github.com/loganknecht>`__), Andrew Cochran,
        Jose Carlos Clemente (`@cleme <https://github.com/cleme>`__), Damien
        Coy, Levi McCracken, Andrew Butterfield, Will Van Treuren (`@wdwvt1
        <https://github.com/wdwvt1>`__), Justin Kuczynski (`@justin212k
        <https://github.com/justin212k>`__), Jose Antonio Navas Molina
        (`@josenavas <https://github.com/josenavas>`__) and Matthew Wakefield
        (`@genomematt <https://github.com/genomematt>`__).
        
        Logo
        ----
        
        scikit-bio's logo was created by `Alina Prassas <http://cargocollective.com/alinaprassas>`_.
        scikit-bio's ASCII art tree was created by `@gregcaporaso
        <https://github.com/gregcaporaso>`_. Our text logo was created at `patorjk.com
        <http://patorjk.com/software/taag/>`__.
        
        .. |Build Status| image:: https://travis-ci.org/biocore/scikit-bio.svg?branch=master
           :target: https://travis-ci.org/biocore/scikit-bio
        .. |Coverage Status| image:: https://coveralls.io/repos/biocore/scikit-bio/badge.png
           :target: https://coveralls.io/r/biocore/scikit-bio
        
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
