Metadata-Version: 1.1
Name: biopython
Version: 1.76
Summary: Freely available tools for computational molecular biology.
Home-page: https://biopython.org/
Author: The Biopython Contributors
Author-email: biopython@biopython.org
License: UNKNOWN
Description: .. image:: https://img.shields.io/pypi/v/biopython.svg
           :alt: Biopython on the Python Package Index (PyPI)
           :target: https://pypi.python.org/pypi/biopython
        .. image:: https://img.shields.io/conda/vn/conda-forge/biopython.svg
           :alt: Biopython on the Conda package conda-forge channel
           :target: https://anaconda.org/conda-forge/biopython
        .. image:: https://img.shields.io/travis/biopython/biopython/master.svg?logo=travis
           :alt: Linux testing with TravisCI
           :target: https://travis-ci.org/biopython/biopython/branches
        .. image:: https://img.shields.io/appveyor/ci/biopython/biopython/master.svg?logo=appveyor
           :alt: Windows testing with AppVeyor
           :target: https://ci.appveyor.com/project/biopython/biopython/history
        .. image:: https://img.shields.io/codecov/c/github/biopython/biopython/master.svg
           :alt: TravisCI test coverage
           :target: https://codecov.io/github/biopython/biopython/
        .. image:: http://depsy.org/api/package/pypi/biopython/badge.svg
           :alt: Research software impact on Depsy
           :target: http://depsy.org/package/python/biopython
        
        .. image:: https://github.com/biopython/biopython/raw/master/Doc/images/biopython_logo_m.png
           :alt: The Biopython Project
           :target: http://biopython.org
        
        Biopython README file
        =====================
        
        The Biopython Project is an international association of developers of freely
        available Python tools for computational molecular biology.
        
        Our user-centric documentation is hosted on http://biopython.org including
        the main Biopython Tutorial and Cookbook:
        
        * HTML - http://biopython.org/DIST/docs/tutorial/Tutorial.html
        * PDF - http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
        
        This README file is intended primarily for people interested in working
        with the Biopython source code, either one of the releases from the
        http://biopython.org website, or from our repository on GitHub
        https://github.com/biopython/biopython
        
        The `NEWS <https://github.com/biopython/biopython/blob/master/NEWS.rst>`_
        file summarises the changes in each release of Biopython.
        
        The Biopython package is open source software made available under generous
        terms. Please see the `LICENSE
        <https://github.com/biopython/biopython/blob/master/LICENSE.rst>`_ file for
        further details.
        
        If you use Biopython in work contributing to a scientific publication, we ask
        that you cite our application note (below) or one of the module specific
        publications (listed on our website):
        
        Cock, P.J.A. et al. Biopython: freely available Python tools for computational
        molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3
        http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878
        
        
        For the impatient
        =================
        
        Python 2.7.9 onwards, and Python 3.4 onwards, include the package management
        system "pip" which should allow you to install Biopython (and its dependency
        NumPy if needed), upgrade or uninstall with just one terminal command::
        
            pip install biopython
            pip install --upgrade biopython
            pip uninstall biopython
        
        Since Biopython 1.70 we have provided pre-compiled binary wheel packages on
        PyPI for Linux, Mac OS X and Windows. This means pip install should be quick,
        and not require a compiler.
        
        As a developer or potential contributor, you may wish to download, build and
        install Biopython yourself. This is described below.
        
        
        Python Requirements
        ===================
        
        We currently recommend using Python 3.8 from http://www.python.org
        
        Biopython is currently supported and tested on the following Python
        implementations:
        
        - Python 2.7, 3.4, 3.5, 3.6, 3.7, 3.8 -- see http://www.python.org
        
          Python 3 is the primary development platform for Biopython. We will drop
          support for Python 2.7 in early 2020, in line with the end-of-life or
          sunset date for Python 2.7 itself.
        
        - PyPy2.7 or PyPy3.5 v7.1.1 -- see http://www.pypy.org
        
          Aside from ``Bio.trie`` (which does not compile as ``marshal.h`` is
          currently missing under PyPy), everything should work. Older versions
          of PyPy mostly work too.
        
        - Jython 2.7 -- see http://www.jython.org
        
          We have decided to deprecate support for Jython, but aside from
          ``Bio.Restriction``, modules with C code, or dependent on SQLite3 or NumPy,
          everything should work. There are some known issues with test failures
          which have not yet been resolved.
        
        Biopython 1.68 was our final release to support Python 2.6.
        
        
        Optional Dependencies
        =====================
        
        Biopython requires NumPy (see http://www.numpy.org) which will be installed
        automatically if you install Biopython with pip (see below for compiling
        Biopython yourself).
        
        Depending on which parts of Biopython you plan to use, there are a number of
        other optional Python dependencies, which can be installed later if needed:
        
        - ReportLab, see http://www.reportlab.com/opensource/ (optional)
          This package is only used in ``Bio.Graphics``, so if you do not need this
          functionality, you will not need to install this package.
        
        - matplotlib, see http://matplotlib.org/ (optional)
          ``Bio.Phylo`` uses this package to plot phylogenetic trees.
        
        - networkx, see http://networkx.lanl.gov/ (optional) and
          pygraphviz or pydot, see http://networkx.lanl.gov/pygraphviz/ and
          http://code.google.com/p/pydot/ (optional)
          These packages are used for certain niche functions in ``Bio.Phylo``.
        
        - rdflib, see https://github.com/RDFLib/rdflib (optional)
          This package is used in the CDAO parser under ``Bio.Phylo``.
        
        - psycopg2, see http://initd.org/psycopg/ (optional) or
          PyGreSQL (pgdb), see http://www.pygresql.org/ (optional)
          These packages are used by ``BioSQL`` to access a PostgreSQL database.
        
        - MySQL Connector/Python, see http://dev.mysql.com/downloads/connector/python/
          This package is used by ``BioSQL`` to access a MySQL database, and is
          supported on Python 2 and 3 and PyPy too.
        
        - mysqlclient, see https://github.com/PyMySQL/mysqlclient-python (optional)
          This is a fork of the older MySQLdb and is used by ``BioSQL`` to access a
          MySQL database. It is supported by Python 2.7, Python 3.5 and above, PyPy 2,
          and PyPy 3.
        
        Note that some of these libraries are not available for PyPy or Jython,
        and not all are available for Python 3 yet either.
        
        In addition there are a number of useful third party tools you may wish to
        install such as standalone NCBI BLAST, EMBOSS or ClustalW.
        
        
        Installation From Source
        ========================
        
        We recommend using the pre-compiled binary wheels available on PyPI using::
        
            pip install biopython
        
        However, if you need to compile Biopython yourself, the following are
        required at compile time - unless you are using Jython (support for which is
        deprecated).
        
        - Python including development header files like ``python.h``, which on Linux
          are often not installed by default (trying looking for and installing a
          package named ``python-dev`` or ``python-devel`` as well as the ``python``
          pacakge).
        
        - Appropriate C compiler for your version of Python, for example GCC on Linux,
          MSVC on Windows. For Mac OS X, or as it is now branded, macOS, use Apple's
          command line tools, which can be installed with the terminal command::
        
              xcode-select --install
        
          This will offer to install Apple's XCode development suite - you can, but it
          is not needed and takes a lot of disk space.
        
        Then either download and decompress our source code, or fetch it using git.
        Now change directory to the Biopython source code folder and run::
        
            python setup.py build
            python setup.py test
            sudo python setup.py install
        
        Substitute ``python`` with your specific version, for example ``python3``,
        ``pypy`` or ``jython``.
        
        To exlude tests that require an internet connection (and which may take a long
        time), use the ``--offline`` option::
        
            python setup.py test --offline
        
        If you need to do additional configuration, e.g. changing the install directory
        prefix, please type ``python setup.py``.
        
        
        Testing
        =======
        
        Biopython includes a suite of regression tests to check if everything is
        running correctly. To run the tests, go to the biopython source code
        directory and type::
        
            python setup.py build
            python setup.py test
        
        If you want to skip the online tests (which is recommended when doing repeated
        testing), use::
        
            python setup.py test --offline
        
        Do not panic if you see messages warning of skipped tests::
        
            test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
        
        This most likely means that a package is not installed.  You can
        ignore this if it occurs in the tests for a module that you were not
        planning on using.  If you did want to use that module, please install
        the required dependency and re-run the tests.
        
        Some of the tests may fail due to network issues, this is often down to
        chance or a service outage. If the problem does not go away on
        re-running the tests, you can use the ``--offline`` option.
        
        There is more testing information in the Biopython Tutorial & Cookbook.
        
        
        Experimental code
        =================
        
        Biopython 1.61 introduced a new warning, ``Bio.BiopythonExperimentalWarning``,
        which is used to mark any experimental code included in the otherwise
        stable Biopython releases. Such 'beta' level code is ready for wider
        testing, but still likely to change, and should only be tried by early
        adopters in order to give feedback via the biopython-dev mailing list.
        
        We'd expect such experimental code to reach stable status within one or two
        releases, at which point our normal policies about trying to preserve
        backwards compatibility would apply.
        
        
        Bugs
        ====
        
        While we try to ship a robust package, bugs inevitably pop up.  If you are
        having problems that might be caused by a bug in Biopython, it is possible
        that it has already been identified. Update to the latest release if you are
        not using it already, and retry. If the problem persists, please search our
        bug database and our mailing lists to see if it has already been reported
        (and hopefully fixed), and if not please do report the bug. We can't fix
        problems we don't know about ;)
        
        Issue tracker: https://github.com/biopython/biopython/issues
        
        If you suspect the problem lies within a parser, it is likely that the data
        format has changed and broken the parsing code.  (The text BLAST and GenBank
        formats seem to be particularly fragile.)  Thus, the parsing code in
        Biopython is sometimes updated faster than we can build Biopython releases.
        You can get the most recent parser by pulling the relevant files (e.g. the
        ones in ``Bio.SeqIO`` or ``Bio.Blast``) from our git repository. However, be
        careful when doing this, because the code in github is not as well-tested
        as released code, and may contain new dependencies.
        
        In any bug report, please let us know:
        
        1. Which operating system and hardware (32 bit or 64 bit) you are using
        2. Python version
        3. Biopython version (or git commit/date)
        4. Traceback that occurs (the full error message)
        
        And also ideally:
        
        5. Example code that breaks
        6. A data file that causes the problem
        
        
        Contributing, Bug Reports
        =========================
        
        Biopython is run by volunteers from all over the world, with many types of
        backgrounds. We are always looking for people interested in helping with code
        development, web-site management, documentation writing, technical
        administration, and whatever else comes up.
        
        If you wish to contribute, please first read `CONTRIBUTING.rst
        <https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst>`_ here,
        visit our web site http://biopython.org and join our mailing list:
        http://biopython.org/wiki/Mailing_lists
        
        
        Distribution Structure
        ======================
        
        - ``README.rst``  -- This file.
        - ``NEWS.rst``    -- Release notes and news.
        - ``LICENSE.rst`` -- What you can do with the code.
        - ``CONTRIB.rst`` -- An (incomplete) list of people who helped Biopython in
          one way or another.
        - ``CONTRIBUTING.rst`` -- An overview about how to contribute to Biopython.
        - ``DEPRECATED.rst`` -- Contains information about modules in Biopython that
          were removed or no longer recommended for use, and how to update code that
          uses those modules.
        - ``MANIFEST.in`` -- Configures which files to include in releases.
        - ``setup.py``    -- Installation file.
        - ``Bio/``        -- The main code base code.
        - ``BioSQL/``     -- Code for using Biopython with BioSQL databases.
        - ``Doc/``        -- Documentation.
        - ``Scripts/``    -- Miscellaneous, possibly useful, standalone scripts.
        - ``Tests/``      -- Regression testing code including sample data files.
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: Freely Distributable
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
