From ba38f2cf2c8c846f265eab6bd202dda09c2780cb Mon Sep 17 00:00:00 2001 From: James Hensman Date: Tue, 29 Apr 2014 09:27:16 +0100 Subject: [PATCH] grabbed readme from old devel branch --- README.md | 58 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/README.md b/README.md index 0ff3d890..b7635b0d 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,51 @@ GPy A Gaussian processes framework in Python. +* [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) Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GPy.png) +Getting started +=============== +Installing with pip +------------------- +The simplest way to install GPy is using pip. ubuntu users can do: + + sudo apt-get install python-pip + pip install gpy + +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. + +Ubuntu +------ +For the most part, the developers are using ubuntu. To install the required packages: + + sudo apt-get install python-numpy python-scipy python-matplotlib + +clone this git repository and add it to your path: + + git clone git@github.com:SheffieldML/GPy.git ~/SheffieldML + echo 'PYTHONPATH=$PYTHONPATH:~/SheffieldML' >> ~/.bashrc + + +Windows +------- +On windows, we recommend the ![anaconda python distribution](http://continuum.io/downloads). We've also had luck with ![enthought](http://www.enthought.com). git clone or unzip the source to a suitable directory, and add an approptiate PYTHONPATH environment variable. + +On windows 7 (and possibly earlier versions) there's a bug in scipy version 0.13 which tries to write very long filenames. Reverting to scipy 0.12 seems to do the trick: + + conda install scipy=0.12 + +OSX +--- +Everything appears to work out-of-the box using ![enthought](http://www.enthought.com) on osx Mavericks. Download/clone GPy, and then add GPy to your PYTHONPATH + + git clone git@github.com:SheffieldML/GPy.git ~/SheffieldML + echo 'PYTHONPATH=$PYTHONPATH:~/SheffieldML' >> ~/.profile + Compiling documentation: ======================== @@ -55,3 +94,22 @@ Run nosetests from the root directory of the repository: nosetests -v +Funding Acknowledgements +======================== + +Current support for the GPy software is coming through the following projects. + +* [EU FP7-PEOPLE Project Ref 316861](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/mlpm/) "MLPM2012: Machine Learning for Personalized Medicine" + +* [BBSRC Project No BB/K011197/1](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/recombinant/) "Linking recombinant gene sequence to protein product manufacturability using CHO cell genomic resources" + +* MRC Special Training Fellowship "Bayesian models of expression in the transcriptome for clinical RNA-seq" + +* [EU FP7-KBBE Project Ref 289434](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/biopredyn/) "From Data to Models: New Bioinformatics Methods and Tools for Data-Driven Predictive Dynamic Modelling in Biotechnological Applications" + +* [EU FP7-ICT Project Ref 612139](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/wysiwyd/) "WYSIWYD: What You Say is What You Did" + +Previous support for the GPy software came from the following projects: + +* [BBSRC Project No BB/H018123/2](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/iterative/) "An iterative pipeline of computational modelling and experimental design for uncovering gene regulatory networks in vertebrates" +* [Erasysbio](http://staffwww.dcs.shef.ac.uk/people/N.Lawrence/projects/synergy/) "SYNERGY: Systems approach to gene regulation biology through nuclear receptors"