pyopenms 2.3.0

.. contents:: **Table of Contents**

------------
Introduction
------------

This package contains Python bindings for a large part of the OpenMS library
(http://www.openms.org) for mass spectrometry based proteomics. It thus
provides providing facile access to a feature-rich, open-source algorithm
library for mass-spectrometry based proteomics analysis. These Python bindings
allow raw access to the data-structures and algorithms implemented in OpenMS,
specifically those for file access (mzXML, mzML, TraML, mzIdentML among
others), basic signal processing (smoothing, filtering, de-isotoping and
peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and
SWATH analysis tools).

The pyOpenMS package runs - like OpenMS - on Windows, Linux and OSX.

-----------
Publication
-----------

The pyOpenMS bindings are described in the following publication:

Rost HL, Schmitt U, Aebersold R and Malmstrom L.
pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.
Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

Please also check `the pyOpenMS homepage`_ for updates and links.

------------
Installation
------------

We provide binary packages for Python 3.4, 3.5 and 3.6 on Windows (64 bit) and
Linux (64 bit) as well as Python 2.7 for Linux, which makes the installation
very straightforward with pip. For other platforms, please refer to the
compilation instructions.

Binary installation
===================

The current binaries require numpy **1.7.x**. As we distribute the package as
binary wheels, you should use *pip* for installation::

$ pip install pyopenms

Source installation
===================

Please use the `the pyOpenMS homepage`_ for instructions on how to build pyOpenMS yourself.

---------------------
Questions and Support
---------------------

For questions and feature requests, please use `the OpenMS github page`_ which
contains a bug tracker, a wiki and describes multiple ways to contact the
developers.

------------
Testing
------------

pyOpenMS provides unittests, they are found under ./pyOpenMS/tests/ and can be
executed using nosetests::

$ python run_nose.py

------------
License
------------

pyOpenMS is published under the 3-clause BSD licence, see ./pyOpenMS/License.txt

-------------
Documentation
-------------

pyOpenMS follows the `OpenMS documentation`_ very closely. Additionally, there is also a `pyOpenMS
Manual <http://proteomics.ethz.ch/pyOpenMS_Manual.pdf>`_ available. The online
manual contains a complete record of every wrapped class and function while the
documentation of the corresponding class or function can be inferred from the
OpenMS online documentation.



.. _the pyOpenMS homepage: https://github.com/OpenMS/OpenMS/wiki/pyOpenMS
.. _the OpenMS documentation: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html
.. _the OpenMS github page: https://github.com/OpenMS/OpenMS/