diff --git a/GPy/__version__.py b/GPy/__version__.py index 5becc17c..5c4105cd 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "1.0.0" +__version__ = "1.0.1" diff --git a/GPy/testing/plotting_tests.py b/GPy/testing/plotting_tests.py index 3d5ccbd1..3ab9ad10 100644 --- a/GPy/testing/plotting_tests.py +++ b/GPy/testing/plotting_tests.py @@ -89,6 +89,9 @@ def _image_directories(): cbook.mkdirs(result_dir) return baseline_dir, result_dir +baseline_dir, result_dir = _image_directories() +if not os.path.exists(baseline_dir): + raise SkipTest("Not installed from source, baseline not available. Install from source to test plotting") def _sequenceEqual(a, b): assert len(a) == len(b), "Sequences not same length" @@ -99,7 +102,6 @@ def _notFound(path): raise IOError('File {} not in baseline') def _image_comparison(baseline_images, extensions=['pdf','svg','png'], tol=11): - baseline_dir, result_dir = _image_directories() for num, base in zip(plt.get_fignums(), baseline_images): for ext in extensions: fig = plt.figure(num) diff --git a/MANIFEST.in b/MANIFEST.in index be80e974..8e665256 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -4,6 +4,7 @@ include doc/source/index.rst include doc/source/tuto*.rst include README.md include README.rst +include AUTHORS.txt # Data and config recursive-include GPy *.json @@ -16,5 +17,5 @@ recursive-include GPy *.h recursive-include GPy *.pyx # Testing -include GPy/testing/baseline/*.png +#include GPy/testing/baseline/*.png #include GPy/testing/pickle_test.pickle diff --git a/README.md b/README.md index e415d58f..db032ea8 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,6 @@ If that is the case, it is best to clean the repo and reinstall. | | Travis-CI | Codecov | RTFD | | ---: | :--: | :---: | :---: | -| **master:** | [![masterstat](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![covmaster](http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=master)](http://codecov.io/github/SheffieldML/GPy?branch=master) | [![docmaster](https://readthedocs.org/projects/gpy/badge/?version=master)](http://gpy.readthedocs.org/en/master/) | | **devel:** | [![develstat](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | [![covdevel](http://codecov.io/github/SheffieldML/GPy/coverage.svg?branch=devel)](http://codecov.io/github/SheffieldML/GPy?branch=devel) | [![docdevel](https://readthedocs.org/projects/gpy/badge/?version=devel)](http://gpy.readthedocs.org/en/devel/) | ## Supported Platforms: diff --git a/README.rst b/README.rst index 596106ab..9436b462 100644 --- a/README.rst +++ b/README.rst @@ -1,263 +1,12 @@ -GPy -=== +# 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 +* GPy [homepage](http://sheffieldml.github.io/GPy/) +* Tutorial [notebooks](http://nbviewer.ipython.org/github/SheffieldML/notebook/blob/master/GPy/index.ipynb) +* User [mailing-list](https://lists.shef.ac.uk/sympa/subscribe/gpy-users) +* Developer [documentation](http://gpy.readthedocs.org/en/devel/) +* Travis-CI [unit-tests](https://travis-ci.org/SheffieldML/GPy) +* [![licence](https://img.shields.io/badge/licence-BSD-blue.svg)](http://opensource.org/licenses/BSD-3-Clause) + +For full description please refer to the [github page](http://sheffieldml.github.io/GPy/) diff --git a/setup.cfg b/setup.cfg index 0e34046b..482ec019 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.0 +current_version = 1.0.1 tag = False commit = True diff --git a/setup.py b/setup.py index 9e0a2bf2..450cf4fd 100644 --- a/setup.py +++ b/setup.py @@ -57,7 +57,7 @@ def read_to_rst(fname): except ImportError: return read(fname) -desc = read_to_rst('README.md') +#desc = read_to_rst('README.md') version_dummy = {} exec(read('GPy/__version__.py'), version_dummy) @@ -143,7 +143,7 @@ setup(name = 'GPy', include_package_data = True, py_modules = ['GPy.__init__'], test_suite = 'GPy.testing', - long_description=desc, + #long_description=desc, install_requires=['numpy>=1.7', 'scipy>=0.16', 'six', 'paramz'], extras_require = {'docs':['sphinx'], 'optional':['mpi4py',