From 747d24d2fa44502caf61efcc2cebbbb16bfb9680 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Thu, 13 Oct 2016 12:19:59 +0100 Subject: [PATCH 01/15] chg: added polynomial basis func kernel --- GPy/kern/src/basis_funcs.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/GPy/kern/src/basis_funcs.py b/GPy/kern/src/basis_funcs.py index 5d589aa61..bbd6ab171 100644 --- a/GPy/kern/src/basis_funcs.py +++ b/GPy/kern/src/basis_funcs.py @@ -102,6 +102,26 @@ def _K(self, X, X2): phi2 = phi2[:, None] return phi1.dot(phi2.T) +class PolinomialBasisFuncKernel(BasisFuncKernel): + def __init__(self, input_dim, degree, variance=1., active_dims=None, ARD=True, name='polinomial_basis'): + """ + A linear segment transformation. The segments start at start, \ + are then linear to stop and constant again. The segments are + normalized, so that they have exactly as much mass above + as below the origin. + + Start and stop can be tuples or lists of starts and stops. + Behaviour of start stop is as np.where(X Date: Thu, 13 Oct 2016 12:21:47 +0100 Subject: [PATCH 02/15] new: gitchangelogrc --- .gitchangelog.rc | 191 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 191 insertions(+) create mode 100644 .gitchangelog.rc diff --git a/.gitchangelog.rc b/.gitchangelog.rc new file mode 100644 index 000000000..1e8ac0882 --- /dev/null +++ b/.gitchangelog.rc @@ -0,0 +1,191 @@ +## +## Format +## +## ACTION: [AUDIENCE:] COMMIT_MSG [!TAG ...] +## +## Description +## +## ACTION is one of 'chg', 'fix', 'new' +## +## Is WHAT the change is about. +## +## 'chg' is for refactor, small improvement, cosmetic changes... +## 'fix' is for bug fixes +## 'new' is for new features, big improvement +## +## AUDIENCE is optional and one of 'dev', 'usr', 'pkg', 'test', 'doc' +## +## Is WHO is concerned by the change. +## +## 'dev' is for developpers (API changes, refactors...) +## 'usr' is for final users (UI changes) +## 'pkg' is for packagers (packaging changes) +## 'test' is for testers (test only related changes) +## 'doc' is for doc guys (doc only changes) +## +## COMMIT_MSG is ... well ... the commit message itself. +## +## TAGs are additionnal adjective as 'refactor' 'minor' 'cosmetic' +## +## They are preceded with a '!' or a '@' (prefer the former, as the +## latter is wrongly interpreted in github.) Commonly used tags are: +## +## 'refactor' is obviously for refactoring code only +## 'minor' is for a very meaningless change (a typo, adding a comment) +## 'cosmetic' is for cosmetic driven change (re-indentation, 80-col...) +## 'wip' is for partial functionality but complete subfunctionality. +## +## Example: +## +## new: usr: support of bazaar implemented +## chg: re-indentend some lines !cosmetic +## new: dev: updated code to be compatible with last version of killer lib. +## fix: pkg: updated year of licence coverage. +## new: test: added a bunch of test around user usability of feature X. +## fix: typo in spelling my name in comment. !minor +## +## Please note that multi-line commit message are supported, and only the +## first line will be considered as the "summary" of the commit message. So +## tags, and other rules only applies to the summary. The body of the commit +## message will be displayed in the changelog without reformatting. + + +## +## ``ignore_regexps`` is a line of regexps +## +## Any commit having its full commit message matching any regexp listed here +## will be ignored and won't be reported in the changelog. +## +ignore_regexps = [ + r'@minor', r'!minor', + r'@cosmetic', r'!cosmetic', + r'@refactor', r'!refactor', + r'@wip', r'!wip', + r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*[p|P]kg:', + r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*[d|D]ev:', + r'^(.{3,3}\s*:)?\s*[fF]irst commit.?\s*$', + ] + + +## ``section_regexps`` is a list of 2-tuples associating a string label and a +## list of regexp +## +## Commit messages will be classified in sections thanks to this. Section +## titles are the label, and a commit is classified under this section if any +## of the regexps associated is matching. +## +section_regexps = [ + ('New', [ + r'^[nN]ew\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$', + ]), + ('Changes', [ + r'^[cC]hg\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$', + ]), + ('Fix', [ + r'^[fF]ix\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$', + ]), + + ('Other', None ## Match all lines + ), + +] + + +## ``body_process`` is a callable +## +## This callable will be given the original body and result will +## be used in the changelog. +## +## Available constructs are: +## +## - any python callable that take one txt argument and return txt argument. +## +## - ReSub(pattern, replacement): will apply regexp substitution. +## +## - Indent(chars=" "): will indent the text with the prefix +## Please remember that template engines gets also to modify the text and +## will usually indent themselves the text if needed. +## +## - Wrap(regexp=r"\n\n"): re-wrap text in separate paragraph to fill 80-Columns +## +## - noop: do nothing +## +## - ucfirst: ensure the first letter is uppercase. +## (usually used in the ``subject_process`` pipeline) +## +## - final_dot: ensure text finishes with a dot +## (usually used in the ``subject_process`` pipeline) +## +## - strip: remove any spaces before or after the content of the string +## +## Additionally, you can `pipe` the provided filters, for instance: +#body_process = Wrap(regexp=r'\n(?=\w+\s*:)') | Indent(chars=" ") +#body_process = Wrap(regexp=r'\n(?=\w+\s*:)') +#body_process = noop +body_process = ReSub(r'((^|\n)[A-Z]\w+(-\w+)*: .*(\n\s+.*)*)+$', r'') | strip + + +## ``subject_process`` is a callable +## +## This callable will be given the original subject and result will +## be used in the changelog. +## +## Available constructs are those listed in ``body_process`` doc. +subject_process = (strip | + ReSub(r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n@]*)(@[a-z]+\s+)*$', r'\4') | + ucfirst | final_dot) + + +## ``tag_filter_regexp`` is a regexp +## +## Tags that will be used for the changelog must match this regexp. +## +tag_filter_regexp = r'^v[0-9]+\.[0-9]+(\.[0-9]+)?$' + + +## ``unreleased_version_label`` is a string +## +## This label will be used as the changelog Title of the last set of changes +## between last valid tag and HEAD if any. +unreleased_version_label = "Unreleased" + + +## ``output_engine`` is a callable +## +## This will change the output format of the generated changelog file +## +## Available choices are: +## +## - rest_py +## +## Legacy pure python engine, outputs ReSTructured text. +## This is the default. +## +## - mustache() +## +## Template name could be any of the available templates in +## ``templates/mustache/*.tpl``. +## Requires python package ``pystache``. +## Examples: +## - mustache("markdown") +## - mustache("restructuredtext") +## +## - makotemplate() +## +## Template name could be any of the available templates in +## ``templates/mako/*.tpl``. +## Requires python package ``mako``. +## Examples: +## - makotemplate("restructuredtext") +## +#output_engine = rest_py +#output_engine = mustache("restructuredtext") +output_engine = mustache("markdown") +#output_engine = makotemplate("restructuredtext") + + +## ``include_merge`` is a boolean +## +## This option tells git-log whether to include merge commits in the log. +## The default is to include them. +include_merge = True From 0007eccd79fafdcde177e9ac30866b41d25811ba Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Thu, 13 Oct 2016 12:23:34 +0100 Subject: [PATCH 03/15] fix: pkg: minor fixes (imports and empty spaces) --- GPy/kern/src/kern.py | 1 - GPy/kern/src/rbf.py | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/GPy/kern/src/kern.py b/GPy/kern/src/kern.py index 537d0f7c0..931591fd5 100644 --- a/GPy/kern/src/kern.py +++ b/GPy/kern/src/kern.py @@ -3,7 +3,6 @@ import sys import numpy as np from ...core.parameterization.parameterized import Parameterized -from paramz.core.observable_array import ObsAr from paramz.caching import Cache_this from .kernel_slice_operations import KernCallsViaSlicerMeta from functools import reduce diff --git a/GPy/kern/src/rbf.py b/GPy/kern/src/rbf.py index 5f3fc97ac..9059ccc03 100644 --- a/GPy/kern/src/rbf.py +++ b/GPy/kern/src/rbf.py @@ -42,6 +42,7 @@ def dK2_drdr(self, r): def dK2_drdr_diag(self): return -self.variance # as the diagonal of r is always filled with zeros + def __getstate__(self): dc = super(RBF, self).__getstate__() if self.useGPU: From 7977a69dca827adc6ef7269243365ecfac0729d4 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Thu, 13 Oct 2016 12:31:39 +0100 Subject: [PATCH 04/15] new: added ploy basis kernel tests and import --- GPy/kern/__init__.py | 2 +- GPy/kern/src/basis_funcs.py | 6 +++--- GPy/testing/kernel_tests.py | 7 +++++++ 3 files changed, 11 insertions(+), 4 deletions(-) diff --git a/GPy/kern/__init__.py b/GPy/kern/__init__.py index 164b66b7d..d82399109 100644 --- a/GPy/kern/__init__.py +++ b/GPy/kern/__init__.py @@ -32,7 +32,7 @@ from .src.splitKern import SplitKern,DEtime from .src.splitKern import DEtime as DiffGenomeKern from .src.spline import Spline -from .src.basis_funcs import LogisticBasisFuncKernel, LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel +from .src.basis_funcs import LogisticBasisFuncKernel, LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel, PolynomialBasisFuncKernel from .src.grid_kerns import GridRBF from .src.sde_matern import sde_Matern32 diff --git a/GPy/kern/src/basis_funcs.py b/GPy/kern/src/basis_funcs.py index bbd6ab171..569a12f19 100644 --- a/GPy/kern/src/basis_funcs.py +++ b/GPy/kern/src/basis_funcs.py @@ -102,8 +102,8 @@ def _K(self, X, X2): phi2 = phi2[:, None] return phi1.dot(phi2.T) -class PolinomialBasisFuncKernel(BasisFuncKernel): - def __init__(self, input_dim, degree, variance=1., active_dims=None, ARD=True, name='polinomial_basis'): +class PolynomialBasisFuncKernel(BasisFuncKernel): + def __init__(self, input_dim, degree, variance=1., active_dims=None, ARD=True, name='polynomial_basis'): """ A linear segment transformation. The segments start at start, \ are then linear to stop and constant again. The segments are @@ -114,7 +114,7 @@ def __init__(self, input_dim, degree, variance=1., active_dims=None, ARD=True, n Behaviour of start stop is as np.where(X Date: Wed, 19 Oct 2016 15:56:10 +0100 Subject: [PATCH 05/15] Added pep.py -- Sparse Gaussian processes using Power Expectation Propagation This allows interpolation between FITC (EP or alpha = 1), and Titsias's variational (VarDTC, VFE when alpha = 0). Reference: A Unifying Framework for Sparse Gaussian Process Approximation using Power Expectation Propagation https://arxiv.org/abs/1605.07066 --- .../latent_function_inference/pep.py | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 GPy/inference/latent_function_inference/pep.py diff --git a/GPy/inference/latent_function_inference/pep.py b/GPy/inference/latent_function_inference/pep.py new file mode 100644 index 000000000..79706292e --- /dev/null +++ b/GPy/inference/latent_function_inference/pep.py @@ -0,0 +1,93 @@ +from .posterior import Posterior +from ...util.linalg import jitchol, tdot, dtrtrs, dtrtri, pdinv +from ...util import diag +import numpy as np +from . import LatentFunctionInference +log_2_pi = np.log(2*np.pi) + +class PEP(LatentFunctionInference): + ''' + Sparse Gaussian processes using Power-Expectation Propagation + for regression: alpha \approx 0 gives VarDTC and alpha = 1 gives FITC + + Reference: A Unifying Framework for Sparse Gaussian Process Approximation using + Power Expectation Propagation, https://arxiv.org/abs/1605.07066 + + ''' + const_jitter = 1e-6 + + def __init__(self, alpha): + super(PEP, self).__init__() + self.alpha = alpha + + def inference(self, kern, X, Z, likelihood, Y, mean_function=None, Y_metadata=None): + assert mean_function is None, "inference with a mean function not implemented" + + num_inducing, _ = Z.shape + num_data, output_dim = Y.shape + + #make sure the noise is not hetero + sigma_n = likelihood.gaussian_variance(Y_metadata) + if sigma_n.size >1: + raise NotImplementedError("no hetero noise with this implementation of PEP") + + Kmm = kern.K(Z) + Knn = kern.Kdiag(X) + Knm = kern.K(X, Z) + U = Knm + + #factor Kmm + diag.add(Kmm, self.const_jitter) + Kmmi, L, Li, _ = pdinv(Kmm) + + #compute beta_star, the effective noise precision + LiUT = np.dot(Li, U.T) + sigma_star = sigma_n + self.alpha * (Knn - np.sum(np.square(LiUT),0)) + beta_star = 1./sigma_star + + # Compute and factor A + A = tdot(LiUT*np.sqrt(beta_star)) + np.eye(num_inducing) + LA = jitchol(A) + + # back substitute to get b, P, v + URiy = np.dot(U.T*beta_star,Y) + tmp, _ = dtrtrs(L, URiy, lower=1) + b, _ = dtrtrs(LA, tmp, lower=1) + tmp, _ = dtrtrs(LA, b, lower=1, trans=1) + v, _ = dtrtrs(L, tmp, lower=1, trans=1) + tmp, _ = dtrtrs(LA, Li, lower=1, trans=0) + P = tdot(tmp.T) + + alpha_const_term = (1.0-self.alpha) / self.alpha + + #compute log marginal + log_marginal = -0.5*num_data*output_dim*np.log(2*np.pi) + \ + -np.sum(np.log(np.diag(LA)))*output_dim + \ + 0.5*output_dim*(1+alpha_const_term)*np.sum(np.log(beta_star)) + \ + -0.5*np.sum(np.square(Y.T*np.sqrt(beta_star))) + \ + 0.5*np.sum(np.square(b)) + 0.5*alpha_const_term*num_data*np.log(sigma_n) + #compute dL_dR + Uv = np.dot(U, v) + dL_dR = 0.5*(np.sum(U*np.dot(U,P), 1) - (1.0+alpha_const_term)/beta_star + np.sum(np.square(Y), 1) - 2.*np.sum(Uv*Y, 1) \ + + np.sum(np.square(Uv), 1))*beta_star**2 + + # Compute dL_dKmm + vvT_P = tdot(v.reshape(-1,1)) + P + dL_dK = 0.5*(Kmmi - vvT_P) + KiU = np.dot(Kmmi, U.T) + dL_dK += self.alpha * np.dot(KiU*dL_dR, KiU.T) + + # Compute dL_dU + vY = np.dot(v.reshape(-1,1),Y.T) + dL_dU = vY - np.dot(vvT_P, U.T) + dL_dU *= beta_star + dL_dU -= self.alpha * 2.*KiU*dL_dR + + dL_dthetaL = likelihood.exact_inference_gradients(dL_dR) + dL_dthetaL += 0.5*alpha_const_term*num_data / sigma_n + grad_dict = {'dL_dKmm': dL_dK, 'dL_dKdiag':dL_dR * self.alpha, 'dL_dKnm':dL_dU.T, 'dL_dthetaL':dL_dthetaL} + + #construct a posterior object + post = Posterior(woodbury_inv=Kmmi-P, woodbury_vector=v, K=Kmm, mean=None, cov=None, K_chol=L) + + return post, log_marginal, grad_dict From 852e86dddf6bfd871e11c82f3ee31d280e5147a0 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Thu, 27 Oct 2016 12:47:53 +0100 Subject: [PATCH 06/15] fix: pypi changing to pypi.org --- appveyor.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/appveyor.yml b/appveyor.yml index 9e7351c17..3d841915b 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -66,7 +66,7 @@ deploy_script: - echo password:%pip_access% >> %USERPROFILE%\\.pypirc - echo[ - echo [test] >> %USERPROFILE%\\.pypirc -- echo repository:https://testpypi.python.org/pypi >> %USERPROFILE%\\.pypirc +- echo repository:https://test.pypi.org/legacy/ >> %USERPROFILE%\\.pypirc - echo username:maxz >> %USERPROFILE%\\.pypirc - echo password:%pip_access% >> %USERPROFILE%\\.pypirc - ps: >- From d70aa771f4e7a9e5f7b6bcb22eb1a112980834d2 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Thu, 27 Oct 2016 13:54:57 +0100 Subject: [PATCH 07/15] fix: pandoc install under travis osx --- .travis.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.travis.yml b/.travis.yml index 7897b0098..7bc9aa3f5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -28,6 +28,10 @@ before_install: install: - echo $PATH - source install_retry.sh +- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; + then + conda install --yes pandoc + fi; - pip install codecov - pip install coveralls - pip install pypandoc From 508e6c009caba40f54f4dff377bea1bbabbd7e60 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Thu, 27 Oct 2016 14:02:38 +0100 Subject: [PATCH 08/15] fix: pandoc install under travis osx --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 7bc9aa3f5..51b9ca2b4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,7 +30,7 @@ install: - source install_retry.sh - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then - conda install --yes pandoc + conda install --yes pandoc; fi; - pip install codecov - pip install coveralls From df7c7539f924af0a21b909b55a1bf1d3899d7790 Mon Sep 17 00:00:00 2001 From: Thang Bui Date: Thu, 27 Oct 2016 14:39:32 +0100 Subject: [PATCH 09/15] added tests --- .../latent_function_inference/__init__.py | 1 + GPy/testing/pep.py | 92 +++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 GPy/testing/pep.py diff --git a/GPy/inference/latent_function_inference/__init__.py b/GPy/inference/latent_function_inference/__init__.py index 90fbf0f1a..3938a6a48 100644 --- a/GPy/inference/latent_function_inference/__init__.py +++ b/GPy/inference/latent_function_inference/__init__.py @@ -67,6 +67,7 @@ def __setstate__(self, state): from .expectation_propagation import EP, EPDTC from .dtc import DTC from .fitc import FITC +from .pep import PEP from .var_dtc_parallel import VarDTC_minibatch from .var_gauss import VarGauss from .gaussian_grid_inference import GaussianGridInference diff --git a/GPy/testing/pep.py b/GPy/testing/pep.py new file mode 100644 index 000000000..0d159d5db --- /dev/null +++ b/GPy/testing/pep.py @@ -0,0 +1,92 @@ +# Copyright (c) 2014, James Hensman, 2016, Thang Bui +# Licensed under the BSD 3-clause license (see LICENSE.txt) + +import unittest +import numpy as np +import GPy + +class PEPgradienttest(unittest.TestCase): + def setUp(self): + ###################################### + # # 1 dimensional example + + N = 20 + # sample inputs and outputs + self.X1D = np.random.uniform(-3., 3., (N, 1)) + self.Y1D = np.sin(self.X1D) + np.random.randn(N, 1) * 0.05 + + ###################################### + # # 2 dimensional example + + # sample inputs and outputs + self.X2D = np.random.uniform(-3., 3., (N, 2)) + self.Y2D = np.sin(self.X2D[:, 0:1]) * np.sin(self.X2D[:, 1:2]) + np.random.randn(N, 1) * 0.05 + + ####################################### + # # more datapoints, check in alpha limits, the log marginal likelihood + # # is consistent with FITC and VFE/Var_DTC + M = 5 + self.X1 = np.c_[np.linspace(-1., 1., N)] + self.Y1 = np.sin(self.X1) + np.random.randn(N, 1) * 0.05 + self.kernel = GPy.kern.RBF(input_dim=1, lengthscale=0.5, variance=1) + self.Z = np.random.uniform(-1, 1, (M, 1)) + self.lik_noise_var = 0.01 + + def test_pep_1d_gradients(self): + m = GPy.models.SparseGPRegression(self.X1D, self.Y1D) + m.inference_method = GPy.inference.latent_function_inference.PEP(alpha=np.random.rand()) + self.assertTrue(m.checkgrad()) + + def test_pep_2d_gradients(self): + m = GPy.models.SparseGPRegression(self.X2D, self.Y2D) + m.inference_method = GPy.inference.latent_function_inference.PEP(alpha=np.random.rand()) + self.assertTrue(m.checkgrad()) + + def test_pep_vfe_consistency(self): + vfe_model = GPy.models.SparseGPRegression( + self.X1, + self.Y1, + kernel=self.kernel, + Z=self.Z + ) + vfe_model.inference_method = GPy.inference.latent_function_inference.VarDTC() + vfe_model.Gaussian_noise.variance = self.lik_noise_var + vfe_lml = vfe_model.log_likelihood() + + pep_model = GPy.models.SparseGPRegression( + self.X1, + self.Y1, + kernel=self.kernel, + Z=self.Z + ) + pep_model.inference_method = GPy.inference.latent_function_inference.PEP(alpha=1e-5) + pep_model.Gaussian_noise.variance = self.lik_noise_var + pep_lml = pep_model.log_likelihood() + + self.assertAlmostEqual(vfe_lml[0, 0], pep_lml[0], delta=abs(0.01*pep_lml[0])) + + def test_pep_fitc_consistency(self): + fitc_model = GPy.models.SparseGPRegression( + self.X1D, + self.Y1D, + kernel=self.kernel, + Z=self.Z + ) + fitc_model.inference_method = GPy.inference.latent_function_inference.FITC() + fitc_model.Gaussian_noise.variance = self.lik_noise_var + fitc_lml = fitc_model.log_likelihood() + + pep_model = GPy.models.SparseGPRegression( + self.X1D, + self.Y1D, + kernel=self.kernel, + Z=self.Z + ) + pep_model.inference_method = GPy.inference.latent_function_inference.PEP(alpha=1) + pep_model.Gaussian_noise.variance = self.lik_noise_var + pep_lml = pep_model.log_likelihood() + + self.assertAlmostEqual(fitc_lml, pep_lml[0], delta=abs(0.001*pep_lml[0])) + + + From 15db5f48ca388f8dfb6fdb632956456db73d899f Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Sun, 30 Oct 2016 11:36:21 +0000 Subject: [PATCH 10/15] fix: Installation #451 --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 2f1dc25f9..ec18c3387 100644 --- a/setup.py +++ b/setup.py @@ -149,6 +149,7 @@ def ismac(): include_package_data = True, py_modules = ['GPy.__init__'], test_suite = 'GPy.testing', + setup_requires = ['numpy>=1.7'], install_requires = ['numpy>=1.7', 'scipy>=0.16', 'six', 'paramz>=0.6.9'], extras_require = {'docs':['sphinx'], 'optional':['mpi4py', From 323204541e04c5c3ca981188a2d04f4a6a1721ef Mon Sep 17 00:00:00 2001 From: Thang Bui Date: Tue, 1 Nov 2016 16:48:45 +0000 Subject: [PATCH 11/15] fixed seed in pep test script #448 --- GPy/testing/pep.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/GPy/testing/pep.py b/GPy/testing/pep.py index 0d159d5db..2aa6a7848 100644 --- a/GPy/testing/pep.py +++ b/GPy/testing/pep.py @@ -9,6 +9,7 @@ class PEPgradienttest(unittest.TestCase): def setUp(self): ###################################### # # 1 dimensional example + np.random.seed(10) N = 20 # sample inputs and outputs @@ -26,6 +27,7 @@ def setUp(self): # # more datapoints, check in alpha limits, the log marginal likelihood # # is consistent with FITC and VFE/Var_DTC M = 5 + np.random.seed(42) self.X1 = np.c_[np.linspace(-1., 1., N)] self.Y1 = np.sin(self.X1) + np.random.randn(N, 1) * 0.05 self.kernel = GPy.kern.RBF(input_dim=1, lengthscale=0.5, variance=1) From 7b384ae25878171815ccd164dcbddea8b0ec0f2c Mon Sep 17 00:00:00 2001 From: Thang Bui Date: Mon, 7 Nov 2016 09:54:50 +0000 Subject: [PATCH 12/15] renamed pep test scripts --- GPy/testing/{pep.py => pep_tests.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename GPy/testing/{pep.py => pep_tests.py} (100%) diff --git a/GPy/testing/pep.py b/GPy/testing/pep_tests.py similarity index 100% rename from GPy/testing/pep.py rename to GPy/testing/pep_tests.py From 977d33614866dc84459ed0cae570ed200c59fa1a Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 7 Nov 2016 10:50:43 +0000 Subject: [PATCH 13/15] =?UTF-8?q?Bump=20version:=201.5.5=20=E2=86=92=201.5?= =?UTF-8?q?.6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- GPy/__version__.py | 2 +- appveyor.yml | 2 +- setup.cfg | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/GPy/__version__.py b/GPy/__version__.py index 8c118e616..d0113b355 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "1.5.5" +__version__ = "1.5.6" diff --git a/appveyor.yml b/appveyor.yml index 3d841915b..3738ea1d6 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -3,7 +3,7 @@ environment: secure: 8/ZjXFwtd1S7ixd7PJOpptupKKEDhm2da/q3unabJ00= COVERALLS_REPO_TOKEN: secure: d3Luic/ESkGaWnZrvWZTKrzO+xaVwJWaRCEP0F+K/9DQGPSRZsJ/Du5g3s4XF+tS - gpy_version: 1.5.5 + gpy_version: 1.5.6 matrix: - PYTHON_VERSION: 2.7 MINICONDA: C:\Miniconda-x64 diff --git a/setup.cfg b/setup.cfg index 11dee055e..77a46f72e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.5.5 +current_version = 1.5.6 tag = True commit = True From 5d480bfc6845429754c3d36e52377fa24c387e94 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 7 Nov 2016 10:52:23 +0000 Subject: [PATCH 14/15] fix: pkg: gitchangelog rc had missing line --- .gitchangelog.rc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitchangelog.rc b/.gitchangelog.rc index 4bf5ee57e..6e8bed1d2 100644 --- a/.gitchangelog.rc +++ b/.gitchangelog.rc @@ -74,6 +74,7 @@ ignore_regexps = [ ## titles are the label, and a commit is classified under this section if any ## of the regexps associated is matching. ## +section_regexps = [ ('New', [ r'^[nN]ew\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$', ]), @@ -86,7 +87,6 @@ ignore_regexps = [ ('Other', None ## Match all lines ), - ] From daa28f5e60b102442539ab84844ebf0a773ad32c Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 7 Nov 2016 10:54:04 +0000 Subject: [PATCH 15/15] fix: pkg: changelogrc and changelog update --- .gitchangelog.rc | 1 - CHANGELOG.md | 159 +++++++++++++++++++++++++++++++++++++++-------- 2 files changed, 134 insertions(+), 26 deletions(-) diff --git a/.gitchangelog.rc b/.gitchangelog.rc index 6e8bed1d2..8132cf2a7 100644 --- a/.gitchangelog.rc +++ b/.gitchangelog.rc @@ -177,7 +177,6 @@ unreleased_version_label = "Unreleased" ## Examples: ## - makotemplate("restructuredtext") ## ->>>>>>> 287584f0cdac51a674996ff6d7092cc876b25ce6 #output_engine = rest_py #output_engine = mustache("restructuredtext") output_engine = mustache("markdown") diff --git a/CHANGELOG.md b/CHANGELOG.md index e553ffb60..167b4ddca 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,19 +1,86 @@ # Changelog -## v1.5.5 (2016-10-03) +## v1.5.6 (2016-11-07) + +### New + +* Added ploy basis kernel tests and import. [mzwiessele] + +* Gitchangelogrc. [mzwiessele] + +### Changes + +* Added polynomial basis func kernel. [mzwiessele] + +### Fix + +* Installation #451. [Max Zwiessele] + +* Pandoc install under travis osx. [mzwiessele] + +* Pandoc install under travis osx. [mzwiessele] + +* Pypi changing to pypi.org. [mzwiessele] ### Other -* Bump version: 1.5.4 → 1.5.5. [Max Zwiessele] +* Bump version: 1.5.5 → 1.5.6. [mzwiessele] +* Merge pull request #448 from thangbui/devel. [Max Zwiessele] -## v1.5.4 (2016-10-03) + Added pep.py -- Sparse Gaussian processes using Power Expectation Propagation -### New +* Renamed pep test scripts. [Thang Bui] -* Added deployment pull request instructions for developers. [mzwiessele] +* Fixed seed in pep test script #448. [Thang Bui] -* Using gitchangelog to keep track of changes and log new features. [mzwiessele] +* Added tests. [Thang Bui] + +* Added pep.py -- Sparse Gaussian processes using Power Expectation Propagation. [Thang Bui] + + This allows interpolation between FITC (EP or alpha = 1), and Titsias's variational (VarDTC, VFE when alpha = 0). + +* Merge pull request #452 from SheffieldML/setupreq. [Max Zwiessele] + + fix: Installation #451 + +* Merge pull request #447 from SheffieldML/polinomial. [Max Zwiessele] + + Polynomial + +* Merge branch 'devel' into polinomial. [mzwiessele] + +* Merge pull request #449 from SheffieldML/deploy. [Max Zwiessele] + + Deploy + +* Update setup.py. [Mike Croucher] + +* Merge pull request #446 from SheffieldML/devel. [Max Zwiessele] + + newest patch fixing some issues + +* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele] + +* Merge branch 'deploy' into devel. [Max Zwiessele] + +* Merge pull request #442 from SheffieldML/devel. [Max Zwiessele] + + New Major for GPy + +* Merge pull request #426 from SheffieldML/devel. [Max Zwiessele] + + some fixes from issues and beckdaniels warped gp improvements + + +## v1.5.5 (2016-10-03) + +### Other + +* Bump version: 1.5.4 → 1.5.5. [Max Zwiessele] + + +## v1.5.4 (2016-10-03) ### Changes @@ -21,14 +88,10 @@ * Fixed naming in variational priors : [Max Zwiessele] -* Changelog update. [mzwiessele] - ### Fix * Bug in dataset (in fn download_url) which wrongly interprets the Content-Length meta data, and just takes first character. [Michael T Smith] -* What's new update fix #425 in changelog. [mzwiessele] - ### Other * Bump version: 1.5.3 → 1.5.4. [Max Zwiessele] @@ -39,25 +102,14 @@ * Merge branch 'kurtCutajar-devel' into devel. [mzwiessele] -* Bump version: 1.5.2 → 1.5.3. [mzwiessele] - -* Merge branch 'devel' into kurtCutajar-devel. [mzwiessele] - -* Bump version: 1.5.1 → 1.5.2. [mzwiessele] - -* Minor readme changes. [mzwiessele] - -* Bump version: 1.5.0 → 1.5.1. [mzwiessele] - -* Bump version: 1.4.3 → 1.5.0. [mzwiessele] -* Bump version: 1.4.2 → 1.4.3. [mzwiessele] +## v1.5.3 (2016-09-06) -* Bump version: 1.4.1 → 1.4.2. [mzwiessele] +### Other -* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele] +* Bump version: 1.5.2 → 1.5.3. [mzwiessele] -* [kern] fix #440. [mzwiessele] +* Merge branch 'devel' into kurtCutajar-devel. [mzwiessele] * [doc] cleanup. [mzwiessele] @@ -92,6 +144,63 @@ * Added core code for GpSSM and GpGrid. [kcutajar] +## v1.5.2 (2016-09-06) + +### New + +* Added deployment pull request instructions for developers. [mzwiessele] + +### Other + +* Bump version: 1.5.1 → 1.5.2. [mzwiessele] + +* Minor readme changes. [mzwiessele] + + +## v1.5.1 (2016-09-06) + +### Fix + +* What's new update fix #425 in changelog. [mzwiessele] + +### Other + +* Bump version: 1.5.0 → 1.5.1. [mzwiessele] + + +## v1.5.0 (2016-09-06) + +### New + +* Using gitchangelog to keep track of changes and log new features. [mzwiessele] + +### Other + +* Bump version: 1.4.3 → 1.5.0. [mzwiessele] + + +## v1.4.3 (2016-09-06) + +### Changes + +* Changelog update. [mzwiessele] + +### Other + +* Bump version: 1.4.2 → 1.4.3. [mzwiessele] + + +## v1.4.2 (2016-09-06) + +### Other + +* Bump version: 1.4.1 → 1.4.2. [mzwiessele] + +* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele] + +* [kern] fix #440. [mzwiessele] + + ## v1.4.1 (2016-09-06) ### Other