From 19adc4c573fb8dcf5fc52384c10445b530ddfd18 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 16:30:39 +0100 Subject: [PATCH 01/11] Update __init__.py --- GPy/kern/src/psi_comp/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GPy/kern/src/psi_comp/__init__.py b/GPy/kern/src/psi_comp/__init__.py index 55780473..90ceca6b 100644 --- a/GPy/kern/src/psi_comp/__init__.py +++ b/GPy/kern/src/psi_comp/__init__.py @@ -65,4 +65,4 @@ class PSICOMP_Linear(PSICOMP): from . import ssrbf_psi_gpucomp -from rbf_psi_gpucomp import PSICOMP_RBF_GPU +from .rbf_psi_gpucomp import PSICOMP_RBF_GPU From e9fb7c4b9e63d835733f1e87ec51198b186741b2 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 16:43:31 +0100 Subject: [PATCH 02/11] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index b10abd8f..dc6900fb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -65,7 +65,7 @@ deploy: password: secure: "vMEOlP7DQhFJ7hQAKtKC5hrJXFl5BkUt4nXdosWWiw//Kg8E+PPLg88XPI2gqIosir9wwgtbSBBbbwCxkM6uxRNMpoNR8Ixyv9fmSXp4rLl7bbBY768W7IRXKIBjpuEy2brQjoT+CwDDSzUkckHvuUjJDNRvUv8ab4P/qYO1LG4=" on: - #tags: true + tags: true branch: plot_density server: https://testpypi.python.org/pypi distributions: "bdist_wheel sdist bdist_egg" From 5fec5b430ac8265bc9c41fc1faf4c4f35103e13a Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 17:05:25 +0100 Subject: [PATCH 03/11] Update setup.cfg --- setup.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index b9b4452f..81f6635b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.8.8 +current_version = 0.8.9.dev tag = True commit = True @@ -9,4 +9,4 @@ commit = True universal = 1 [upload_docs] -upload-dir = doc/build/html \ No newline at end of file +upload-dir = doc/build/html From a59ea0ddedf647e08b1dbc0f05f7fdb0d8fc8498 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 17:05:56 +0100 Subject: [PATCH 04/11] Update __version__.py --- GPy/__version__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GPy/__version__.py b/GPy/__version__.py index aa00ec3d..7cdc9d27 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "0.8.8" +__version__ = "0.8.9.dev" From 735150d9eb052681835504f3ec8efe1b87feb67c Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 17:28:17 +0100 Subject: [PATCH 05/11] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index dc6900fb..5cbe7c00 100644 --- a/.travis.yml +++ b/.travis.yml @@ -68,5 +68,5 @@ deploy: tags: true branch: plot_density server: https://testpypi.python.org/pypi - distributions: "bdist_wheel sdist bdist_egg" + distributions: "bdist_wheel sdist" skip_cleanup: true From 0b3cb5031a5a301d371494ea575b8765342f3a3e Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 17:57:57 +0100 Subject: [PATCH 06/11] Update setup.cfg --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 81f6635b..6de3462a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.8.9.dev +current_version = 0.8.8dev tag = True commit = True From 199d9472a507ac2d4ef376f34b43fa2fb6ecf2a7 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 17:59:07 +0100 Subject: [PATCH 07/11] Update __version__.py --- GPy/__version__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GPy/__version__.py b/GPy/__version__.py index 7cdc9d27..312cb2a8 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "0.8.9.dev" +__version__ = "0.8.8dev" From 2c9bddd7849db68e1d5ebd3ce33e33b48b9f7de4 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 18:00:05 +0100 Subject: [PATCH 08/11] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 5cbe7c00..527172cf 100644 --- a/.travis.yml +++ b/.travis.yml @@ -67,6 +67,6 @@ deploy: on: tags: true branch: plot_density - server: https://testpypi.python.org/pypi + #server: https://testpypi.python.org/pypi distributions: "bdist_wheel sdist" skip_cleanup: true From 03ad735c314563d94036f4d26cf06bb6ea9ae63b Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 18:53:22 +0100 Subject: [PATCH 09/11] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 527172cf..72e677cd 100644 --- a/.travis.yml +++ b/.travis.yml @@ -66,7 +66,7 @@ deploy: secure: "vMEOlP7DQhFJ7hQAKtKC5hrJXFl5BkUt4nXdosWWiw//Kg8E+PPLg88XPI2gqIosir9wwgtbSBBbbwCxkM6uxRNMpoNR8Ixyv9fmSXp4rLl7bbBY768W7IRXKIBjpuEy2brQjoT+CwDDSzUkckHvuUjJDNRvUv8ab4P/qYO1LG4=" on: tags: true - branch: plot_density + branch: master #server: https://testpypi.python.org/pypi distributions: "bdist_wheel sdist" skip_cleanup: true From 5ee7fb2a97010560d0d98941a97a61f6ed62be0d Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 18:57:57 +0100 Subject: [PATCH 10/11] Update README.md --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 897b5cae..647ba37f 100644 --- a/README.md +++ b/README.md @@ -10,10 +10,10 @@ A Gaussian processes framework in Python. * [![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/) | +| | Travis-CI | Codecov | +| ---: | :--: | :---: | +| **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) | +| **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) | ### Supported Platforms: @@ -55,11 +55,11 @@ If you'd like to install from source, or want to contribute to the project (e.g. If you're having trouble installing GPy via `pip install GPy` here is a probable solution: - git clone https://github.com/mikecroucher/GPy.git + git clone https://github.com/SheffieldML/GPy.git cd GPy git checkout devel - python3 setup.py build_ext --inplace - nosetests3 GPy/testing + python setup.py build_ext --inplace + nosetests GPy/testing ### Direct downloads From eb913aa2a2fc4939892984728f25662ae895c78d Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 11 Oct 2015 19:03:03 +0100 Subject: [PATCH 11/11] Update README.md --- README.md | 96 +++++++++++++++++-------------------------------------- 1 file changed, 30 insertions(+), 66 deletions(-) diff --git a/README.md b/README.md index 647ba37f..e3c2b236 100644 --- a/README.md +++ b/README.md @@ -45,11 +45,13 @@ With anaconda you can install GPy by the following: conda update scipy pip install gpy - -We've also had luck with [enthought](http://www.enthought.com), -although enthought currently (as of 8th Sep. 2015) does not support scipy 0.16. -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. +We've also had luck with [enthought](http://www.enthought.com). Install scipy later or the same as +0.16 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 @@ -63,10 +65,28 @@ If you're having trouble installing GPy via `pip install GPy` here is a probable ### 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) +[![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://pypi.python.org/pypi/GPy) +[![Windows](https://img.shields.io/badge/download-windows-orange.svg)](https://pypi.python.org/pypi/GPy) +[![MacOSX](https://img.shields.io/badge/download-macosx-blue.svg)](https://pypi.python.org/pypi/GPy) +## 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 @@ -82,84 +102,28 @@ clone this git repository and add it to your path: echo 'PYTHONPATH=$PYTHONPATH:~/SheffieldML' >> ~/.bashrc - -### OSX - - -We were working hard to make pre-built distributions ready. -You can now install GPy via pip on MacOSX using -[anaconda python distribution](http://continuum.io/downloads): - - conda update scipy - pip install gpy - -If this does not work, then you need to build GPy yourself, -using the [development toolkits](https://developer.apple.com/xcode/). -Download/clone GPy and run the build process: - - conda update scipy - git clone git@github.com:SheffieldML/GPy.git ~/GPy - cd ~/GPy - python setup.py install - -If you do not wish to build the C extensions (10 times speedup), -you can run the pure python installations, by just adding GPy -to your python path. - - echo 'PYTHONPATH=$PYTHONPATH:~/SheffieldML' >> ~/.profile - - - ### 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 -A LaTeX distribution is also required to compile the equations. Note that the extra packages are necessary to install the unicode packages. To compile the equations to PNG format for use in HTML pages, the package *dvipng* must be installed. IPython is also required. On Debian-based systems, this can be achieved as follows: - - sudo apt-get install texlive texlive-latex-extra texlive-base texlive-recommended - sudo apt-get install dvipng - sudo apt-get install ipython - - -#### Compiling documentation: - +##### 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/ - - -## 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() - - +The HTML files are then stored in doc/build/html ## Funding Acknowledgements