diff --git a/README.rst b/README.rst new file mode 100644 index 00000000..596106ab --- /dev/null +++ b/README.rst @@ -0,0 +1,263 @@ +GPy +=== + +The Gaussian processes framework in Python. + +- GPy `homepage `__ +- Tutorial + `notebooks `__ +- User + `mailing-list `__ +- Developer `documentation `__ +- Travis-CI `unit-tests `__ +- |licence| + +Updated Structure +----------------- + +We have pulled the core parameterization out of GPy. It is a package +called `paramz `__ and is the pure +gradient based model optimization. + +If you installed GPy with pip, just upgrade the package using: + +:: + + $ pip install --upgrade GPy + +If you have the developmental version of GPy (using the develop or -e +option) just install the dependencies by running + +:: + + $ python setup.py develop + +again, in the GPy installation folder. + +A warning: This usually works, but sometimes ``distutils/setuptools`` +opens a whole can of worms here, specially when compiled extensions are +involved. If that is the case, it is best to clean the repo and +reinstall. + +Continuous integration +---------------------- + ++---------------+----------------+---------------+---------------+ +| | Travis-CI | Codecov | RTFD | ++===============+================+===============+===============+ +| **master:** | |masterstat| | |covmaster| | |docmaster| | ++---------------+----------------+---------------+---------------+ +| **devel:** | |develstat| | |covdevel| | |docdevel| | ++---------------+----------------+---------------+---------------+ + +Supported Platforms: +-------------------- + +` `__ +` `__ +` `__ +` `__ + +Python 2.7, 3.3 and higher + +Citation +-------- + +:: + + @Misc{gpy2014, + author = {{The GPy authors}}, + title = {{GPy}: A Gaussian process framework in python}, + howpublished = {\url{http://github.com/SheffieldML/GPy}}, + year = {2012--2015} + } + +Pronounciation: +~~~~~~~~~~~~~~~ + +We like to pronounce it 'g-pie'. + +Getting started: installing with pip +------------------------------------ + +We are now requiring the newest version (0.16) of +`scipy `__ and thus, we strongly recommend using +the `anaconda python distribution `__. +With anaconda you can install GPy by the following: + +:: + + conda update scipy + pip install gpy + +We've also had luck with `enthought `__. +Install scipy 0.16 (or later) and then pip install GPy: + +:: + + pip install gpy + +If you'd like to install from source, or want to contribute to the +project (i.e. by sending pull requests via github), read on. + +Troubleshooting installation problems +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +If you're having trouble installing GPy via ``pip install GPy`` here is +a probable solution: + +:: + + git clone https://github.com/SheffieldML/GPy.git + cd GPy + git checkout devel + python setup.py build_ext --inplace + nosetests GPy/testing + +Direct downloads +~~~~~~~~~~~~~~~~ + +|PyPI version| |source| |Windows| |MacOSX| + +Running unit tests: +------------------- + +Ensure nose is installed via pip: + +:: + + pip install nose + +Run nosetests from the root directory of the repository: + +:: + + nosetests -v GPy/testing + +or from within IPython + +:: + + import GPy; GPy.tests() + +or using setuptools + +:: + + python setup.py test + +Ubuntu hackers +-------------- + + Note: Right now the Ubuntu package index does not include scipy + 0.16.0, and thus, cannot be used for GPy. We hope this gets fixed + soon. + +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 + +Compiling documentation: +------------------------ + +The documentation is stored in doc/ and is compiled with the Sphinx +Python documentation generator, and is written in the reStructuredText +format. + +The Sphinx documentation is available here: +http://sphinx-doc.org/latest/contents.html + +**Installing dependencies:** + +To compile the documentation, first ensure that Sphinx is installed. On +Debian-based systems, this can be achieved as follows: + +:: + + sudo apt-get install python-pip + sudo pip install sphinx + +**Compiling documentation:** + +The documentation can be compiled as follows: + +:: + + cd doc + sphinx-apidoc -o source/ ../GPy/ + make html + +The HTML files are then stored in doc/build/html + +Funding Acknowledgements +------------------------ + +Current support for the GPy software is coming through the following +projects. + +- `EU FP7-HEALTH Project Ref 305626 `__ + "RADIANT: Rapid Development and Distribution of Statistical Tools for + High-Throughput Sequencing Data" + +- `EU FP7-PEOPLE Project Ref + 316861 `__ + "MLPM2012: Machine Learning for Personalized Medicine" + +- MRC Special Training Fellowship "Bayesian models of expression in the + transcriptome for clinical RNA-seq" + +- `EU FP7-ICT Project Ref + 612139 `__ + "WYSIWYD: What You Say is What You Did" + +Previous support for the GPy software came from the following projects: + +- `BBSRC Project No + BB/K011197/1 `__ + "Linking recombinant gene sequence to protein product + manufacturability using CHO cell genomic resources" +- `EU FP7-KBBE Project Ref + 289434 `__ + "From Data to Models: New Bioinformatics Methods and Tools for + Data-Driven Predictive Dynamic Modelling in Biotechnological + Applications" +- `BBSRC Project No + BB/H018123/2 `__ + "An iterative pipeline of computational modelling and experimental + design for uncovering gene regulatory networks in vertebrates" +- `Erasysbio `__ + "SYNERGY: Systems approach to gene regulation biology through nuclear + receptors" + +.. |licence| image:: https://img.shields.io/badge/licence-BSD-blue.svg + :target: http://opensource.org/licenses/BSD-3-Clause +.. |masterstat| image:: https://travis-ci.org/SheffieldML/GPy.svg?branch=master + :target: https://travis-ci.org/SheffieldML/GPy +.. |covmaster| image:: http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=master + :target: http://codecov.io/github/SheffieldML/GPy?branch=master +.. |docmaster| image:: https://readthedocs.org/projects/gpy/badge/?version=master + :target: http://gpy.readthedocs.org/en/master/ +.. |develstat| image:: https://travis-ci.org/SheffieldML/GPy.svg?branch=devel + :target: https://travis-ci.org/SheffieldML/GPy +.. |covdevel| image:: http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=devel + :target: http://codecov.io/github/SheffieldML/GPy?branch=devel +.. |docdevel| image:: https://readthedocs.org/projects/gpy/badge/?version=devel + :target: http://gpy.readthedocs.org/en/devel/ +.. |PyPI version| image:: https://badge.fury.io/py/GPy.svg + :target: https://pypi.python.org/pypi/GPy +.. |source| image:: https://img.shields.io/badge/download-source-green.svg + :target: https://pypi.python.org/pypi/GPy +.. |Windows| image:: https://img.shields.io/badge/download-windows-orange.svg + :target: https://pypi.python.org/pypi/GPy +.. |MacOSX| image:: https://img.shields.io/badge/download-macosx-blue.svg + :target: https://pypi.python.org/pypi/GPy diff --git a/setup.cfg b/setup.cfg index d393931e..0e34046b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -11,3 +11,6 @@ universal = 1 [upload_docs] upload-dir = doc/build/html +[metadata] +description-file = README.rst +