From 5ff46838834d233ec56ccb2a1db6558f1ace5362 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Fri, 11 Sep 2015 17:26:38 +0100 Subject: [PATCH 01/20] [geepie] ? --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index db40350a..1e67b0ac 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GP ### Pronounciation -We like to pronounce it 'Gee-pie'. +We like to pronounce it 'dʒí páj'. ### Getting started: installing with pip From 4a1cd7c12cf1cd6844b3da10c42bc20eab2d108c Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Fri, 11 Sep 2015 17:34:06 +0100 Subject: [PATCH 02/20] [README] updated readme instructions, added troubleshooting --- README.md | 29 ++++++++--------------------- 1 file changed, 8 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 1e67b0ac..0bffec7e 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,10 @@ A Gaussian processes framework in Python. Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GPy.png) +### Avalability + +Python 2.7 and 3.4, Windows, MacOSX, Linux + ### Citation @Misc{gpy2014, @@ -20,9 +24,9 @@ Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GP year = {2012--2015} } -### Pronounciation +### Pronounciation: dʒí páj -We like to pronounce it 'dʒí páj'. +We like to pronounce it 'g-pie'. ### Getting started: installing with pip @@ -39,12 +43,9 @@ 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. -### 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 @@ -52,20 +53,6 @@ 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! - - - ### Ubuntu hackers > Note: Right now the Ubuntu package index does not include scipy 0.16.0, and thus, cannot From 8a332a4de6a72b23466e3dd7910eb1c6d9ed4eb8 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 12 Sep 2015 12:36:55 +0100 Subject: [PATCH 03/20] Master branch showing in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0bffec7e..f6374b9e 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ A Gaussian processes framework in Python. * [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) +Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master) ### Avalability From 4af4548ffbbd05cc86e14b9c679bfe54b8957c59 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 12 Sep 2015 12:37:58 +0100 Subject: [PATCH 04/20] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f6374b9e..e9fa2f00 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,9 @@ A Gaussian processes framework in Python. * [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.svg?branch=master) +### Continuous integration: +- *master*: ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master) +- *devel*: ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel) ### Avalability From eb7276c37df596467942e2d31d8163add7ce791f Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 12 Sep 2015 12:42:06 +0100 Subject: [PATCH 05/20] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e9fa2f00..23bbf08c 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ A Gaussian processes framework in Python. * [Unit tests (Travis-CI)](https://travis-ci.org/SheffieldML/GPy) ### Continuous integration: -- *master*: ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master) -- *devel*: ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel) +|**master**| ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)| +|**devel** | ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel) | ### Avalability From 72d822d62742bec307da6fe5d1cef6c7f6918110 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 12 Sep 2015 12:44:54 +0100 Subject: [PATCH 06/20] Update README.md --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 23bbf08c..23ff8530 100644 --- a/README.md +++ b/README.md @@ -9,9 +9,12 @@ A Gaussian processes framework in Python. * [Online documentation](https://gpy.readthedocs.org/en/latest/) * [Unit tests (Travis-CI)](https://travis-ci.org/SheffieldML/GPy) -### Continuous integration: -|**master**| ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)| -|**devel** | ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel) | +##### Continuous integration: + + +| master | devel | +| ---------- | --------- | +| ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)| ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel) | ### Avalability From 37e835aa36b18c32bc500684cc10dd2b74240e1f Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 12 Sep 2015 14:39:16 +0100 Subject: [PATCH 07/20] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 23ff8530..0333ef1f 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,12 @@ A Gaussian processes framework in Python. * [Online documentation](https://gpy.readthedocs.org/en/latest/) * [Unit tests (Travis-CI)](https://travis-ci.org/SheffieldML/GPy) -##### Continuous integration: +##### Continuous integration: | master | devel | | ---------- | --------- | -| ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)| ![CI status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel) | +| [![Build Status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![Build Status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | ### Avalability From 9b5f9e99b63548878f5a175da260e382b1231982 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 13 Sep 2015 17:23:01 +0100 Subject: [PATCH 08/20] Update README.md --- README.md | 33 +++++++++++++++++++++++++-------- 1 file changed, 25 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 0333ef1f..3a29e627 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,5 @@ # GPy - A Gaussian processes framework in Python. * [GPy homepage](http://sheffieldml.github.io/GPy/) @@ -8,18 +7,30 @@ 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) +* [![licence](https://img.shields.io/badge/licence-BSD-blue.svg)](http://opensource.org/licenses/BSD-3-Clause) -##### Continuous integration: +#### Continuous integration +| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | +| ---: | :--: | +| **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | -| master | devel | -| ---------- | --------- | -| [![Build Status](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![Build Status](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | + -### Avalability +### Availability: -Python 2.7 and 3.4, Windows, MacOSX, Linux +Supported python versions: 2.7, 3.x +----- +[](https://www.python.org/) [](http://www.microsoft.com/en-gb/windows) [](http://www.apple.com/osx/) [](https://en.wikipedia.org/wiki/List_of_Linux_distributions) + +----- ### Citation @Misc{gpy2014, @@ -33,7 +44,7 @@ Python 2.7 and 3.4, Windows, MacOSX, Linux 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 @@ -58,6 +69,12 @@ If you're having trouble installing GPy via `pip install GPy` here is a probable python3 setup.py build_ext --inplace nosetests3 GPy/testing +### 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 > Note: Right now the Ubuntu package index does not include scipy 0.16.0, and thus, cannot From 85a97786ed12f83dcf6b2ca18c6ff917ef35a3ae Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 13 Sep 2015 17:24:25 +0100 Subject: [PATCH 09/20] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3a29e627..1f80987d 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ $.ajax({ Supported python versions: 2.7, 3.x ----- -[](https://www.python.org/) [](http://www.microsoft.com/en-gb/windows) [](http://www.apple.com/osx/) [](https://en.wikipedia.org/wiki/List_of_Linux_distributions) +[](https://www.python.org/) [](http://www.microsoft.com/en-gb/windows) [](http://www.apple.com/osx/) [](https://en.wikipedia.org/wiki/List_of_Linux_distributions) ----- ### Citation From c99c0cc6bf6bf9ba2e84a854d541887f68ccc3c1 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 13 Sep 2015 17:26:10 +0100 Subject: [PATCH 10/20] Update README.md --- README.md | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 1f80987d..83975950 100644 --- a/README.md +++ b/README.md @@ -15,22 +15,14 @@ A Gaussian processes framework in Python. | ---: | :--: | | **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | - - ### Availability: -Supported python versions: 2.7, 3.x +Supported python versions: 2.7, 3.3 and higher ------ [](https://www.python.org/) [](http://www.microsoft.com/en-gb/windows) [](http://www.apple.com/osx/) [](https://en.wikipedia.org/wiki/List_of_Linux_distributions) +---- + ------ ### Citation @Misc{gpy2014, From 5a09caf4573b544e1787211599ad0d3e485770c5 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 13 Sep 2015 17:27:29 +0100 Subject: [PATCH 11/20] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 83975950..cd041511 100644 --- a/README.md +++ b/README.md @@ -15,13 +15,13 @@ A Gaussian processes framework in Python. | ---: | :--: | | **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | -### Availability: - -Supported python versions: 2.7, 3.3 and higher +### Supported Platforms: [](https://www.python.org/) [](http://www.microsoft.com/en-gb/windows) [](http://www.apple.com/osx/) [](https://en.wikipedia.org/wiki/List_of_Linux_distributions) ---- +Python 2.7, 3.3 and higher + ### Citation From 3392a4f5c1c9d47760c7a0a1ee7953361809f94c Mon Sep 17 00:00:00 2001 From: Zhenwen Dai Date: Fri, 18 Sep 2015 13:41:45 +0100 Subject: [PATCH 12/20] add adadelta as an optimizer --- GPy/core/model.py | 2 +- GPy/inference/optimization/optimization.py | 24 +++++++++++++++++++++- 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/GPy/core/model.py b/GPy/core/model.py index 9d8b89f4..8c00667e 100644 --- a/GPy/core/model.py +++ b/GPy/core/model.py @@ -255,7 +255,7 @@ class Model(Parameterized): opt.model = self else: optimizer = optimization.get_optimizer(optimizer) - opt = optimizer(start, model=self, max_iters=max_iters, **kwargs) + opt = optimizer(x_init=start, model=self, max_iters=max_iters, **kwargs) with VerboseOptimization(self, opt, maxiters=max_iters, verbose=messages, ipython_notebook=ipython_notebook, clear_after_finish=clear_after_finish) as vo: opt.run(f_fp=self._objective_grads, f=self._objective, fp=self._grads) diff --git a/GPy/inference/optimization/optimization.py b/GPy/inference/optimization/optimization.py index 48bdd809..9aab1bec 100644 --- a/GPy/inference/optimization/optimization.py +++ b/GPy/inference/optimization/optimization.py @@ -228,13 +228,35 @@ class opt_SCG(Optimizer): self.f_opt = self.trace[-1] self.funct_eval = opt_result[2] self.status = opt_result[3] + +class Opt_Adadelta(Optimizer): + def __init__(self, step_rate=0.1, decay=0.9, momentum=0, *args, **kwargs): + Optimizer.__init__(self, *args, **kwargs) + self.opt_name = "Adadelta (climin)" + self.step_rate=step_rate + self.decay = decay + self.momentum = momentum + + def opt(self, f_fp=None, f=None, fp=None): + assert not fp is None + + import climin + + opt = climin.adadelta.Adadelta(self.x_init, fp, step_rate=self.step_rate, decay=self.decay, momentum=self.momentum) + + for info in opt: + if info['n_iter']>=self.max_iters: + self.x_opt = opt.wrt + self.status = 'maximum number of function evaluations exceeded ' + break def get_optimizer(f_min): optimizers = {'fmin_tnc': opt_tnc, 'simplex': opt_simplex, 'lbfgsb': opt_lbfgsb, - 'scg': opt_SCG} + 'scg': opt_SCG, + 'adadelta':Opt_Adadelta} if rasm_available: optimizers['rasmussen'] = opt_rasm From 61c4502b1880cd3082db1800296452a09b4e12da Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Fri, 18 Sep 2015 17:12:25 +0100 Subject: [PATCH 13/20] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index cd041511..ec9397ab 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 - -| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | +| | Travis-CI | Readthedocs | | ---: | :--: | -| **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | +| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | https://readthedocs.org/projects/pip/badge/?version=master | +| **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | https://readthedocs.org/projects/pip/badge/?version=devel | ### Supported Platforms: From ab1d6ac4f3e6a2a1ff02a89f2f02bc0115543b27 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Fri, 18 Sep 2015 17:16:02 +0100 Subject: [PATCH 14/20] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ec9397ab..e2bb0408 100644 --- a/README.md +++ b/README.md @@ -11,9 +11,9 @@ A Gaussian processes framework in Python. #### Continuous integration | | Travis-CI | Readthedocs | -| ---: | :--: | -| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | https://readthedocs.org/projects/pip/badge/?version=master | -| **devel:** | [![devel](https://travis-ci.org/SheffieldML/GPy.svg?branch=devel)](https://travis-ci.org/SheffieldML/GPy) | https://readthedocs.org/projects/pip/badge/?version=devel | +| ---: | :--: | :---: | +| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![mdocs](https://img.shields.io/badge/docs-master-yellow.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) | [![ddocs](https://img.shields.io/badge/docs-devel-yellow.svg?style=flat)](http://gpy.readthedocs.org/en/devel/) | ### Supported Platforms: From 7120880695e9dad853343ca573df39859c540fec Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Fri, 18 Sep 2015 17:16:21 +0100 Subject: [PATCH 15/20] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e2bb0408..6c13a7f7 100644 --- a/README.md +++ b/README.md @@ -12,8 +12,8 @@ A Gaussian processes framework in Python. #### Continuous integration | | Travis-CI | Readthedocs | | ---: | :--: | :---: | -| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![mdocs](https://img.shields.io/badge/docs-master-yellow.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) | [![ddocs](https://img.shields.io/badge/docs-devel-yellow.svg?style=flat)](http://gpy.readthedocs.org/en/devel/) | +| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![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) | [![ddocs](https://img.shields.io/badge/docs-devel-blue.svg?style=flat)](http://gpy.readthedocs.org/en/devel/) | ### Supported Platforms: From c7a25f8ed1b51068ec13da1aa6fa4808dcc70661 Mon Sep 17 00:00:00 2001 From: Zhenwen Dai Date: Fri, 18 Sep 2015 20:31:08 +0100 Subject: [PATCH 16/20] Add RADIANT grant to funding acknowledgements --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 6c13a7f7..1a1f1ef4 100644 --- a/README.md +++ b/README.md @@ -166,6 +166,8 @@ or from within IPython 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" From 1e3ad59f5e488f4e06837ce8aaaad7731e355ce7 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Thu, 1 Oct 2015 08:03:01 +0100 Subject: [PATCH 17/20] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 1a1f1ef4..87580b4f 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 | Readthedocs | -| ---: | :--: | :---: | -| **master:** | [![master](https://travis-ci.org/SheffieldML/GPy.svg?branch=master)](https://travis-ci.org/SheffieldML/GPy) | [![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) | [![ddocs](https://img.shields.io/badge/docs-devel-blue.svg?style=flat)](http://gpy.readthedocs.org/en/devel/) | +| | 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: From 55fb393751321dd029aaa5c3b52d1911d852f40f Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 10 Oct 2015 23:13:08 +0100 Subject: [PATCH 18/20] Update pickle_tests.py --- GPy/testing/pickle_tests.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/GPy/testing/pickle_tests.py b/GPy/testing/pickle_tests.py index 64357b39..d4d96a24 100644 --- a/GPy/testing/pickle_tests.py +++ b/GPy/testing/pickle_tests.py @@ -59,14 +59,17 @@ class Test(ListDictTestCase): f.seek(0) pio2 = pickle.load(f) self.assertListDictEquals(pio._properties, pio2._properties) - - with tempfile.TemporaryFile('w+b') as f: + + f = tempfile.TemporaryFile('w+b') + + with f: pickle.dump(piov, f) f.seek(0) - pio2 = pickle.load(f) - #py3 fix - #self.assertListDictEquals(dict(piov.items()), dict(pio2.iteritems())) - self.assertListDictEquals(dict(piov.items()), dict(pio2.items())) + + pio2 = GPy.load(f) + #py3 fix + #self.assertListDictEquals(dict(piov.items()), dict(pio2.iteritems())) + self.assertListDictEquals(dict(piov.items()), dict(pio2.items())) def test_param(self): param = Param('test', np.arange(4*2).reshape(4,2)) From 2a01e9008a6414feca031032f7b15109236e7d46 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 10 Oct 2015 23:21:41 +0100 Subject: [PATCH 19/20] Update pickle_tests.py --- GPy/testing/pickle_tests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GPy/testing/pickle_tests.py b/GPy/testing/pickle_tests.py index d4d96a24..ad3c4f0b 100644 --- a/GPy/testing/pickle_tests.py +++ b/GPy/testing/pickle_tests.py @@ -22,6 +22,7 @@ from GPy.models.gp_regression import GPRegression from functools import reduce from GPy.util.caching import Cacher from pickle import PicklingError +import GPy def toy_model(): X = np.linspace(0,1,50)[:, None] @@ -64,8 +65,7 @@ class Test(ListDictTestCase): with f: pickle.dump(piov, f) - f.seek(0) - + pio2 = GPy.load(f) #py3 fix #self.assertListDictEquals(dict(piov.items()), dict(pio2.iteritems())) From 4cf70ea132e4d82c4c9a106079bd98ebb35054f6 Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sat, 10 Oct 2015 23:27:50 +0100 Subject: [PATCH 20/20] Update pickle_tests.py --- GPy/testing/pickle_tests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GPy/testing/pickle_tests.py b/GPy/testing/pickle_tests.py index ad3c4f0b..17e29377 100644 --- a/GPy/testing/pickle_tests.py +++ b/GPy/testing/pickle_tests.py @@ -65,8 +65,8 @@ class Test(ListDictTestCase): with f: pickle.dump(piov, f) - - pio2 = GPy.load(f) + f.seek(0) + pio2 = pickle.load(f) #py3 fix #self.assertListDictEquals(dict(piov.items()), dict(pio2.iteritems())) self.assertListDictEquals(dict(piov.items()), dict(pio2.items()))