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# GPy
A Gaussian processes framework in Python.
* [GPy homepage](http://sheffieldml.github.io/GPy/)
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* [User mailing list](https://lists.shef.ac.uk/sympa/subscribe/gpy-users)
* [Online documentation](https://gpy.readthedocs.org/en/latest/)
* [Unit tests (Travis-CI)](https://travis-ci.org/SheffieldML/GPy)
* [![licence](https://img.shields.io/badge/licence-BSD-blue.svg)](http://opensource.org/licenses/BSD-3-Clause)
#### Continuous integration
| | Travis-CI | Codecov | Readthedocs |
| ---: | :--: | :---: | :---: |
| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![codecov.io](http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=master)](http://codecov.io/github/SheffieldML/GPy?branch=master) | [![mdocs](https://img.shields.io/badge/docs-master-blue.svg?style=flat)](http://gpy.readthedocs.org/en/master/) |
| **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | [![codecov.io](http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=devel)](http://codecov.io/github/SheffieldML/GPy?branch=devel) | [![ddocs](https://img.shields.io/badge/docs-devel-blue.svg?style=flat)](http://gpy.readthedocs.org/en/devel/) |
### Supported Platforms:
[<img src="https://www.python.org/static/community_logos/python-logo-generic.svg" height="40">](https://www.python.org/) [<img src="https://upload.wikimedia.org/wikipedia/commons/5/5f/Windows_logo_-_2012.svg" height="40">](http://www.microsoft.com/en-gb/windows) [<img src="https://upload.wikimedia.org/wikipedia/commons/8/8e/OS_X-Logo.svg" height="40">](http://www.apple.com/osx/) [<img src="https://upload.wikimedia.org/wikipedia/commons/3/35/Tux.svg" height="40">](https://en.wikipedia.org/wiki/List_of_Linux_distributions)
----
Python 2.7, 3.3 and higher
Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GPy.png)
### Citation
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year = {2012--2015}
}
### Pronounciation
### Pronounciation: dʒí páj
We like to pronounce it 'Gee-pie'.
We like to pronounce it 'g-pie'.
### Getting started: installing with pip
### Getting started: installing with pip
We are now requiring the newest version (0.16) of
[scipy](http://www.scipy.org/) and thus, we strongly recommend using
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If you'd like to install from source, or want to contribute to the project (e.g. by sending pull requests via github), read on.
### Python 3 Compatibility
Work is underway to make GPy run on Python 3.
### Troubleshooting installation problems
* All tests in the testsuite now run on Python3.
To see this for yourself, in Ubuntu 14.04, you can do
If you're having trouble installing GPy via `pip install GPy` here is a probable solution:
git clone https://github.com/mikecroucher/GPy.git
cd GPy
@ -52,19 +61,11 @@ To see this for yourself, in Ubuntu 14.04, you can do
python3 setup.py build_ext --inplace
nosetests3 GPy/testing
nosetests3 is Ubuntu's way of reffering to the Python 3 version of nosetests. You install it with
sudo apt-get install python3-nose
The command `python3 setup.py build_ext --inplace` builds the Cython extensions. IF it doesn't work, you may need to install this:
sudo apt-get install python3-dev
* Test coverage is less than 100% so it is expected that there is still more work to be done. We need more tests and examples to try out.
* All weave functions not covered by the test suite are *simply commented out*. Can add equivalents later as test functions become available
* A set of benchmarks would be useful!
### Direct downloads
[![PyPI version](https://badge.fury.io/py/GPy.svg)](https://pypi.python.org/pypi/GPy) [![source](https://img.shields.io/badge/download-source-green.svg)](https://github.com/SheffieldML/GPy/releases/latest)
[![Windows](https://img.shields.io/badge/download-windows-orange.svg)](https://github.com/SheffieldML/GPy/releases/latest)
[![MacOSX](https://img.shields.io/badge/download-macosx-blue.svg)](https://github.com/SheffieldML/GPy/releases/latest)
### Ubuntu hackers
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Current support for the GPy software is coming through the following projects.
* [EU FP7-HEALTH Project Ref 305626](http://radiant-project.eu) "RADIANT: Rapid Development and Distribution of Statistical Tools for High-Throughput Sequencing Data"
* [EU FP7-PEOPLE Project Ref 316861](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/mlpm/) "MLPM2012: Machine Learning for Personalized Medicine"
* MRC Special Training Fellowship "Bayesian models of expression in the transcriptome for clinical RNA-seq"