From 80b6d798b796e7ab86f1119539a092ac654adec9 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:17:02 +0100 Subject: [PATCH 01/10] fix: paramz version for parallel optimization fix --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 318545b5..55f81762 100644 --- a/setup.py +++ b/setup.py @@ -150,7 +150,7 @@ setup(name = 'GPy', 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'], + install_requires = ['numpy>=1.7', 'scipy>=0.16', 'six', 'paramz>=0.7.4'], extras_require = {'docs':['sphinx'], 'optional':['mpi4py', 'ipython>=4.0.0', From 98ecb4196b9e8a78f485f9fa6902dff479107505 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:17:30 +0100 Subject: [PATCH 02/10] fix: pkg: changelog --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5c7f5031..ba1306bb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## Unreleased + +### Fix + +* Paramz version for parallel optimization fix. [mzwiessele] + + ## v1.7.3 (2017-06-19) ### Fix From d2551b75c1b87b570959097fe00b6ee7f3745e2e Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:19:00 +0100 Subject: [PATCH 03/10] =?UTF-8?q?Bump=20version:=201.7.3=20=E2=86=92=201.7?= =?UTF-8?q?.4?= 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 008aaa97..acbbc1ce 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "1.7.3" +__version__ = "1.7.4" diff --git a/appveyor.yml b/appveyor.yml index 575ffa9f..9503fccc 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: 1.7.3 + gpy_version: 1.7.4 matrix: - PYTHON_VERSION: 2.7 MINICONDA: C:\Miniconda-x64 diff --git a/setup.cfg b/setup.cfg index cba06241..656867db 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.7.3 +current_version = 1.7.4 tag = True commit = True From 5074a94f1d304bcb9d0410f9e9adc0658ec85161 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:19:16 +0100 Subject: [PATCH 04/10] fix: pkg: changelog --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba1306bb..76dcc144 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,15 @@ # Changelog -## Unreleased +## v1.7.4 (2017-06-19) ### Fix * Paramz version for parallel optimization fix. [mzwiessele] +### Other + +* Bump version: 1.7.3 → 1.7.4. [mzwiessele] + ## v1.7.3 (2017-06-19) From 2820ddfdf7edc5f990726e40d3db8f9b5ed4107e Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:31:14 +0100 Subject: [PATCH 05/10] fix: splitting forecast tests into 3 to circumvent 10 minute stop of travis --- GPy/testing/gpy_kernels_state_space_tests.py | 101 +++++++++++++++---- 1 file changed, 81 insertions(+), 20 deletions(-) diff --git a/GPy/testing/gpy_kernels_state_space_tests.py b/GPy/testing/gpy_kernels_state_space_tests.py index f39eb9d0..c06093dd 100644 --- a/GPy/testing/gpy_kernels_state_space_tests.py +++ b/GPy/testing/gpy_kernels_state_space_tests.py @@ -306,11 +306,7 @@ class StateSpaceKernelsTests(np.testing.TestCase): gp_kernel=gp_kernel, mean_compare_decimal=2, var_compare_decimal=2) - def test_forecast(self,): - """ - Test time-series forecasting. - """ - + def test_forecast_regular(self,): # Generate data -> np.random.seed(339) # seed the random number generator #import pdb; pdb.set_trace() @@ -334,37 +330,102 @@ class StateSpaceKernelsTests(np.testing.TestCase): #import pdb; pdb.set_trace() - def get_new_kernels(): - periodic_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) - gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + periodic_kernel - gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) - gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) + periodic_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + periodic_kernel + gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) - periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) - ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + \ - GPy.kern.sde_Bias(1, active_dims=[0,]) + periodic_kernel + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + \ + GPy.kern.sde_Bias(1, active_dims=[0,]) + periodic_kernel - ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) - ss_kernel.std_periodic.period.constrain_bounded(0.15, 100) + ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + ss_kernel.std_periodic.period.constrain_bounded(0.15, 100) - return ss_kernel, gp_kernel - - ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'regular', use_cython=False, optimize_max_iters=30, check_gradients=True, predict_X=X_test, gp_kernel=gp_kernel, mean_compare_decimal=2, var_compare_decimal=2) + def test_forecast_svd(self,): + # Generate data -> + np.random.seed(339) # seed the random number generator + #import pdb; pdb.set_trace() + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=5.0, noise_var=2.0, + plot = False, points_num=100, x_interval = (0, 40), random=True) + + (X1,Y1) = generate_linear_data(x_points=X, tangent=1.0, add_term=20.0, noise_var=0.0, + plot = False, points_num=100, x_interval = (0, 40), random=True) + + Y = Y + Y1 + + X_train = X[X <= 20] + Y_train = Y[X <= 20] + X_test = X[X > 20] + Y_test = Y[X > 20] + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + X_train.shape = (X_train.shape[0],1); Y_train.shape = (Y_train.shape[0],1) + X_test.shape = (X_test.shape[0],1); Y_test.shape = (Y_test.shape[0],1) + # Generate data <- + + #import pdb; pdb.set_trace() + + periodic_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + periodic_kernel + gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) + + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + \ + GPy.kern.sde_Bias(1, active_dims=[0,]) + periodic_kernel + + ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + ss_kernel.std_periodic.period.constrain_bounded(0.15, 100) - ss_kernel, gp_kernel = get_new_kernels() self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'svd', use_cython=False, optimize_max_iters=30, check_gradients=False, predict_X=X_test, gp_kernel=gp_kernel, mean_compare_decimal=2, var_compare_decimal=2) - ss_kernel, gp_kernel = get_new_kernels() + def test_forecast_svd_cython(self,): + # Generate data -> + np.random.seed(339) # seed the random number generator + #import pdb; pdb.set_trace() + (X,Y) = generate_sine_data(x_points=None, sin_period=5.0, sin_ampl=5.0, noise_var=2.0, + plot = False, points_num=100, x_interval = (0, 40), random=True) + + (X1,Y1) = generate_linear_data(x_points=X, tangent=1.0, add_term=20.0, noise_var=0.0, + plot = False, points_num=100, x_interval = (0, 40), random=True) + + Y = Y + Y1 + + X_train = X[X <= 20] + Y_train = Y[X <= 20] + X_test = X[X > 20] + Y_test = Y[X > 20] + + X.shape = (X.shape[0],1); Y.shape = (Y.shape[0],1) + X_train.shape = (X_train.shape[0],1); Y_train.shape = (Y_train.shape[0],1) + X_test.shape = (X_test.shape[0],1); Y_test.shape = (Y_test.shape[0],1) + # Generate data <- + + #import pdb; pdb.set_trace() + + periodic_kernel = GPy.kern.StdPeriodic(1,active_dims=[0,]) + gp_kernel = GPy.kern.Linear(1, active_dims=[0,]) + GPy.kern.Bias(1, active_dims=[0,]) + periodic_kernel + gp_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + gp_kernel.std_periodic.period.constrain_bounded(0.15, 100) + + periodic_kernel = GPy.kern.sde_StdPeriodic(1,active_dims=[0,]) + ss_kernel = GPy.kern.sde_Linear(1,X,active_dims=[0,]) + \ + GPy.kern.sde_Bias(1, active_dims=[0,]) + periodic_kernel + + ss_kernel.std_periodic.lengthscale.constrain_bounded(0.25, 1000) + ss_kernel.std_periodic.period.constrain_bounded(0.15, 100) + self.run_for_model(X_train, Y_train, ss_kernel, kalman_filter_type = 'svd', use_cython=True, optimize_max_iters=30, check_gradients=False, predict_X=X_test, From cc4456eb4d1f87ffb20d9a7957e4235ca1b718b8 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:31:57 +0100 Subject: [PATCH 06/10] =?UTF-8?q?Bump=20version:=201.7.4=20=E2=86=92=201.7?= =?UTF-8?q?.5?= 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 acbbc1ce..b8ebaa6a 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "1.7.4" +__version__ = "1.7.5" diff --git a/appveyor.yml b/appveyor.yml index 9503fccc..adf00c4f 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: 1.7.4 + gpy_version: 1.7.5 matrix: - PYTHON_VERSION: 2.7 MINICONDA: C:\Miniconda-x64 diff --git a/setup.cfg b/setup.cfg index 656867db..72d69258 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.7.4 +current_version = 1.7.5 tag = True commit = True From e3094f2ede511d333da87aee7af82e0480946b6d Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:32:11 +0100 Subject: [PATCH 07/10] fix: pkg: changelog --- CHANGELOG.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 76dcc144..4dd71c67 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## v1.7.5 (2017-06-19) + +### Fix + +* Splitting forecast tests into 3 to circumvent 10 minute stop of travis. [mzwiessele] + +### Other + +* Bump version: 1.7.4 → 1.7.5. [mzwiessele] + + ## v1.7.4 (2017-06-19) ### Fix From ad02c948fa8a42dc79f59f4e2935c9cde142f54d Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:34:27 +0100 Subject: [PATCH 08/10] fix: appveyor not uploading to testpypi for now --- appveyor.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/appveyor.yml b/appveyor.yml index adf00c4f..fe9d69e0 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -72,16 +72,17 @@ deploy_script: - echo username = maxz >> %USERPROFILE%\\.pypirc - echo password = %pip_access% >> %USERPROFILE%\\.pypirc - ps: >- - if ($env:APPVEYOR_REPO_BRANCH -eq 'devel') { - twine upload --skip-existing -r test dist/* - } - elseif ($env:APPVEYOR_REPO_BRANCH -eq 'deploy') { + if ($env:APPVEYOR_REPO_BRANCH -eq 'deploy') { twine upload --skip-existing dist/* } else { echo not deploying on other branches } +# if ($env:APPVEYOR_REPO_BRANCH -eq 'devel') { +# twine upload --skip-existing -r test dist/* +# } # This is for testing the upload to testpypi, it causes a fail, so we will undo it here + # deploy: # - provider: GitHub # release: GPy-v$(gpy_version) From 3379293bab28a608900809841f39321bf45f33ae Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:34:35 +0100 Subject: [PATCH 09/10] =?UTF-8?q?Bump=20version:=201.7.5=20=E2=86=92=201.7?= =?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 b8ebaa6a..462db014 100644 --- a/GPy/__version__.py +++ b/GPy/__version__.py @@ -1 +1 @@ -__version__ = "1.7.5" +__version__ = "1.7.6" diff --git a/appveyor.yml b/appveyor.yml index fe9d69e0..81ef6af6 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: 1.7.5 + gpy_version: 1.7.6 matrix: - PYTHON_VERSION: 2.7 MINICONDA: C:\Miniconda-x64 diff --git a/setup.cfg b/setup.cfg index 72d69258..4fec0562 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.7.5 +current_version = 1.7.6 tag = True commit = True From a2de712ba34a18a3298f04abe3240c1afe9db5a7 Mon Sep 17 00:00:00 2001 From: mzwiessele Date: Mon, 19 Jun 2017 13:35:25 +0100 Subject: [PATCH 10/10] fix: pkg: changelog --- CHANGELOG.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4dd71c67..6b1a8a65 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## v1.7.6 (2017-06-19) + +### Fix + +* Appveyor not uploading to testpypi for now. [mzwiessele] + +### Other + +* Bump version: 1.7.5 → 1.7.6. [mzwiessele] + + ## v1.7.5 (2017-06-19) ### Fix