From 987b0ab75a6b8d9143940d4e3263794589cf70ee Mon Sep 17 00:00:00 2001 From: Neil Lawrence Date: Tue, 8 Sep 2015 20:57:34 +0100 Subject: [PATCH 1/5] Update AUTHORS.txt --- AUTHORS.txt | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/AUTHORS.txt b/AUTHORS.txt index 31efef02..c1599265 100644 --- a/AUTHORS.txt +++ b/AUTHORS.txt @@ -1,8 +1,3 @@ -James Hensman -Nicolo Fusi -Ricardo Andrade -Nicolas Durrande -Alan Saul -Max Zwiessele -Neil D. Lawrence -Zhenwen Dai +# This list was out of date, I've put "see contributors" for the moment. Not sure how to fix long term but don't want to be +# embarrassed by some off the great contributors of late being omitted from a list. +See contributors. From bc01eaa84accceca0199aae9f47c3866fb45f75a Mon Sep 17 00:00:00 2001 From: Neil Lawrence Date: Tue, 8 Sep 2015 21:00:52 +0100 Subject: [PATCH 2/5] Update README.md --- README.md | 19 ++++--------------- 1 file changed, 4 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index c9a6c708..34238dac 100644 --- a/README.md +++ b/README.md @@ -14,10 +14,10 @@ Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GP ### Citation @Misc{gpy2014, - author = {The GPy authors}, + author = {{The GPy authors}}, title = {{GPy}: A Gaussian process framework in python}, howpublished = {\url{http://github.com/SheffieldML/GPy}}, - year = {2012--2014} + year = {2012--2015} } ### Pronounciation @@ -69,14 +69,6 @@ The command `python3 setup.py build_ext --inplace` builds the Cython extensions. * 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! -### Citation - - @Misc{gpy2014, - author = {The GPy authors}, - title = {{GPy}: A Gaussian process framework in python}, - howpublished = {\url{http://github.com/SheffieldML/GPy}}, - year = {2012--2014} - } ### Pronounciation @@ -165,15 +157,12 @@ 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/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" +* [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" * [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" From 65377716497df0e4f063d36a507255d7e4237a8d Mon Sep 17 00:00:00 2001 From: Zhenwen Dai Date: Tue, 8 Sep 2015 21:38:48 +0100 Subject: [PATCH 3/5] bug fix for compilation on Mac --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ef51cd3e..93217fb4 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ def ismac(): if ismac(): compile_flags = [ '-O3', ] - link_args = [''] + link_args = [] else: compile_flags = [ '-fopenmp', '-O3', ] link_args = ['-lgomp'] From a4db6d68a6b7fc56d91a01608a0b58e0c8cf272e Mon Sep 17 00:00:00 2001 From: Zhenwen Dai Date: Tue, 8 Sep 2015 22:11:17 +0100 Subject: [PATCH 4/5] bug fix for the print function in samplers.py --- GPy/inference/mcmc/samplers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GPy/inference/mcmc/samplers.py b/GPy/inference/mcmc/samplers.py index 7ca6a4c6..12939cfe 100644 --- a/GPy/inference/mcmc/samplers.py +++ b/GPy/inference/mcmc/samplers.py @@ -41,7 +41,7 @@ class Metropolis_Hastings: self.model._log_det_jacobian() accepted = np.zeros(Ntotal,dtype=np.bool) for it in range(Ntotal): - print "sample %d of %d\r"%(it,Ntotal), + print("sample %d of %d\r"%(it,Ntotal),end="\t") sys.stdout.flush() prop = np.random.multivariate_normal(current, self.cov*self.scale*self.scale) self.model.optimizer_array = prop From e93726669d0995b5d4ac615f682fb7e4237bb20e Mon Sep 17 00:00:00 2001 From: mikecroucher Date: Wed, 9 Sep 2015 00:20:47 +0100 Subject: [PATCH 5/5] Update setup.py with new version number --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 93217fb4..0d97f9f0 100644 --- a/setup.py +++ b/setup.py @@ -7,7 +7,7 @@ from setuptools import setup, Extension import numpy as np # Version number -version = '0.6.1' +version = '0.8' def read(fname): return open(os.path.join(os.path.dirname(__file__), fname)).read()