mirror of
https://github.com/SheffieldML/GPy.git
synced 2026-06-08 15:05:15 +02:00
Zhenwen Dai
GitHub
commit
e4848ce3ad
20 changed files with 45687 additions and 23959 deletions
1
.gitignore
vendored
1
.gitignore
vendored
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@ -1,6 +1,7 @@
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*.py[cod]
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# C extensions
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*_cython.c
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*.so
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# Packages
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@ -19,7 +19,7 @@ env:
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#- PYTHON_VERSION=3.4
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- PYTHON_VERSION=3.5
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- PYTHON_VERSION=3.6
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#- PYTHON_VERSION=3.7
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- PYTHON_VERSION=3.7
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before_install:
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- wget https://github.com/mzwiessele/travis_scripts/raw/master/download_miniconda.sh
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262
CHANGELOG.md
262
CHANGELOG.md
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@ -1,24 +1,146 @@
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# Changelog
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## v1.9.6 (2018-10-30)
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## New
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## v1.9.8 (2019-05-17)
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* Added a new class that enables using multiple likelihoods [@esiivola]
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### Fix
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* Alex grig kalman new [@AlexGrig, @mzwiessele]
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* Also run on 3.5. [mzwiessele]
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## Fix
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### Other
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* fix typo in docstring for GP.opimize() [@RobRomijnders]
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* Bump version: 1.9.7 → 1.9.8. [mzwiessele]
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* Updates to posterior sampling [@lawrennd]
|
||||
* Pkg: changelog. [mzwiessele]
|
||||
|
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* Jayanthkoushik cython fix [@jayanthkoushik, @mzwiessele]
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* Added missing columns (:), fixed indentation [@vlavorini]
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## v1.9.7 (2019-05-17)
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|
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### Fix
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* Version. [mzwiessele]
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* Plotting. [mzwiessele]
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* Matplotlib 2.0 mlba -> cbook: [mzwiessele]
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### Other
|
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|
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* Bump version: 1.9.6 → 1.9.7. [mzwiessele]
|
||||
|
||||
* Merge branch 'deploy' into devel. [mzwiessele]
|
||||
|
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* Merge pull request #703 from SheffieldML/devel. [Zhenwen Dai]
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|
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Deploy the version 1.9.6
|
||||
|
||||
* Merge pull request #709 from KOLANICH/ignoring_cython-generated_C_sources. [Zhenwen Dai]
|
||||
|
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Cython-generated files should be regenerated
|
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|
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* Cython-generated files should be regenerated. [KOLANICH]
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|
||||
* Merge pull request #758 from marpulli/py37_travis. [Zhenwen Dai]
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|
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Add travis build for 3.7, remove for 3.5, bump version to 1.9.7
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|
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* Bump version to 1.9.7. [Mark Pullin]
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|
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* Move python 3.5 build to 3.7. [Mark Pullin]
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|
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* Update README.md. [Mike Smith]
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|
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* I've added these steps to install necessary libraries. [Mike Smith]
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||||
|
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Lots of people seem to have this problem with an "error: command 'gcc' failed with exit status 1" on installing.
|
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E.g. this can be reproduced on a clean AWS Ubuntu install.
|
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Feel free to revert, but this issue comes up regularly.
|
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|
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* Merge pull request #722 from jopago/devel. [Zhenwen Dai]
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|
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Add to_dict methods to White and Brownian kernels
|
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|
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* Update static.py. [Joan Gonzalvez]
|
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|
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* Update brownian.py. [Joan Gonzalvez]
|
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|
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added to_dict method
|
||||
|
||||
* Merge pull request #718 from KOLANICH/patch-1. [Zhenwen Dai]
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|
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Don't import `datasets` by default since it is almost never needed
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|
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* Don't import datasets by default since it is almost never needed. [KOLANICH]
|
||||
|
||||
* Merge pull request #708 from KOLANICH/cython_code_fix. [Zhenwen Dai]
|
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|
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Integer division is needed here.
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|
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* Integer division is needed here. [KOLANICH]
|
||||
|
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* Fix the bug due to changes in Numpy (#744) [Zhenwen Dai]
|
||||
|
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* Merge pull request #719 from ajgpitch/install_fixes. [Max Zwiessele]
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FIXES - for installing under Python 3.7
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|
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* Recythonised c files. [Alexander Pitchford]
|
||||
|
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* Merge branch 'fix-state_space_cython-misc' into install_fixes. [Alexander Pitchford]
|
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|
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* Type fixed - Q_square_root_dict. [Alexander Pitchford]
|
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|
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* Merge branch 'fix-state_space_cython-misc' into install_fixes. [Alexander Pitchford]
|
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|
||||
* Merge branch 'devel' into fix-state_space_cython-misc. [Alexander Pitchford]
|
||||
|
||||
* Merge branch 'build_ext-source_pyx' into install_fixes. [Alexander Pitchford]
|
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|
||||
* Merge branch 'devel' into build_ext-source_pyx. [Alexander Pitchford]
|
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|
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* Merge branch 'fix-cython-import_array' into install_fixes. [Alexander Pitchford]
|
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|
||||
* Merge branch 'devel' into fix-cython-import_array. [Alexander Pitchford]
|
||||
|
||||
* Fix the version number in appveyor.yml. [Zhenwen Dai]
|
||||
|
||||
* Fix the version number in setup.cfg. [Dai]
|
||||
|
||||
* Merge branch 'deploy' into devel. [Zhenwen Dai]
|
||||
|
||||
* Merge pull request #656 from SheffieldML/devel. [Max Zwiessele]
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||||
|
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push PR to deploy
|
||||
|
||||
* Bump the version: 1.9.5 -> 1.9.6. [Zhenwen Dai]
|
||||
|
||||
* Merge pull request #691 from vlavorini/devel. [Zhenwen Dai]
|
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|
||||
Added missing columns (:), fixed indentation
|
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|
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* Added missing columns (:), fixed indentation. [Vincenzo Lavorini]
|
||||
|
||||
* Fix the bug in the prediction of full covariance matrix (#702) [Zhenwen Dai]
|
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|
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* fix the bug in the prediction of full covariance matrix
|
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|
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* Fix the test cases.
|
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|
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* update the version requirement for matplotlib
|
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|
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* Merge branch 'build_ext-source_pyx' into install_fixes. [Alexander Pitchford]
|
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|
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* Ext sources changed to pyx. [Alexander Pitchford]
|
||||
|
||||
* Merge branch 'fix-cython-import_array' into install_fixes. [Alexander Pitchford]
|
||||
|
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* Np.import_array() added to files where cimport numpy used. [Alexander Pitchford]
|
||||
|
||||
* Add missing colons and fix indentation. [Alexander Pitchford]
|
||||
|
||||
* Pkg: changelog. [mzwiessele]
|
||||
|
||||
* Fix the bug in the prediction of full covariance matrix [@zhenwendai]
|
||||
|
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## v1.9.5 (2018-09-02)
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@ -2503,8 +2625,8 @@
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* Merge branch 'devel' into paramz. [mzwiessele]
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|
||||
Conflicts:
|
||||
GPy/core/parameterization/parameter_core.py
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||||
GPy/testing/pickle_tests.py
|
||||
GPy/core/parameterization/parameter_core.py
|
||||
GPy/testing/pickle_tests.py
|
||||
|
||||
* [paramz] wrapping - todo: deprecation warnings. [mzwiessele]
|
||||
|
||||
|
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@ -4017,7 +4139,7 @@
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|||
* Merge remote-tracking branch 'upstream/devel' into devel. [tjhgit]
|
||||
|
||||
Conflicts:
|
||||
GPy/kern/__init__.py
|
||||
GPy/kern/__init__.py
|
||||
|
||||
* Added spline kernel (from P. Hennig) to GPy. [tjhgit]
|
||||
|
||||
|
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@ -5552,10 +5674,10 @@
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|||
* Integrated Laplace and merged Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/gp.py
|
||||
GPy/likelihoods/__init__.py
|
||||
GPy/likelihoods/likelihood_functions.py
|
||||
GPy/likelihoods/link_functions.py
|
||||
GPy/core/gp.py
|
||||
GPy/likelihoods/__init__.py
|
||||
GPy/likelihoods/likelihood_functions.py
|
||||
GPy/likelihoods/link_functions.py
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||||
|
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* Fixed white variance. [Alan Saul]
|
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|
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|
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@ -5694,7 +5816,7 @@
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|||
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/inference/latent_function_inference/inferenceX.py
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||||
GPy/inference/latent_function_inference/inferenceX.py
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|
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* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
|
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|
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@ -6209,7 +6331,7 @@
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* [dim red plots] plotting big models. [mzwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/plotting/matplot_dep/dim_reduction_plots.py
|
||||
GPy/plotting/matplot_dep/dim_reduction_plots.py
|
||||
|
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* Add debug util module and try to debug sparsegp_mpi. [Zhenwen Dai]
|
||||
|
||||
|
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@ -6226,8 +6348,8 @@
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|||
* [normalizer] first commit for normalizer in GPy. [mzwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/sparse_gp.py
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||||
GPy/models/bayesian_gplvm.py
|
||||
GPy/core/sparse_gp.py
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GPy/models/bayesian_gplvm.py
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||||
|
||||
* Further bug fix for sparsegp_mpi. [Zhenwen Dai]
|
||||
|
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|
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@ -6246,8 +6368,8 @@
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|||
* [ard] enhanced ard handling and plotting. [mzwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/kern/_src/linear.py
|
||||
GPy/models/ss_gplvm.py
|
||||
GPy/kern/_src/linear.py
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GPy/models/ss_gplvm.py
|
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|
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* [linear] einsums. [mzwiessele]
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||||
|
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|
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@ -6350,14 +6472,14 @@
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* [inference] less constant jitter, and jitter adjustements. [mzwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/util/linalg.py
|
||||
GPy/util/linalg.py
|
||||
|
||||
* Fixed a bug in optimize restarts: it now used optimizer_array. [James Hensman]
|
||||
|
||||
* [vardtc missing] logging. [maxz]
|
||||
|
||||
Conflicts:
|
||||
GPy/inference/latent_function_inference/var_dtc.py
|
||||
GPy/inference/latent_function_inference/var_dtc.py
|
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|
||||
* [init] normalization bugfix. [mzwiessele]
|
||||
|
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|
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@ -6858,7 +6980,7 @@
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|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/kern/_src/kern.py
|
||||
GPy/kern/_src/kern.py
|
||||
|
||||
* Missing file, import line commented. [Ricardo]
|
||||
|
||||
|
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@ -6907,8 +7029,8 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/models/gp_classification.py
|
||||
GPy/models/sparse_gp_classification.py
|
||||
GPy/models/gp_classification.py
|
||||
GPy/models/sparse_gp_classification.py
|
||||
|
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* New file. [Ricardo]
|
||||
|
||||
|
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@ -7189,7 +7311,7 @@
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|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/likelihoods/mixed_noise.py
|
||||
GPy/likelihoods/mixed_noise.py
|
||||
|
||||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
|
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@ -7274,14 +7396,14 @@
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|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Max Zwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/likelihoods/gaussian.py
|
||||
GPy/likelihoods/gaussian.py
|
||||
|
||||
* Bug fix w.r.t. var_dtc.py. [Zhenwen Dai]
|
||||
|
||||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/inference/latent_function_inference/var_dtc.py
|
||||
GPy/inference/latent_function_inference/var_dtc.py
|
||||
|
||||
* New model SparseGPCoregionalizedRegression. [Ricardo]
|
||||
|
||||
|
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@ -7481,8 +7603,8 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/gp.py
|
||||
GPy/plotting/matplot_dep/models_plots.py
|
||||
GPy/core/gp.py
|
||||
GPy/plotting/matplot_dep/models_plots.py
|
||||
|
||||
* GPCoregionalizedRegresssion added. [Ricardo]
|
||||
|
||||
|
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@ -7743,7 +7865,7 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/kern/_src/constructors.py
|
||||
GPy/kern/_src/constructors.py
|
||||
|
||||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
|
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@ -7752,8 +7874,8 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/kern/kern.py
|
||||
GPy/kern/parts/prod.py
|
||||
GPy/kern/kern.py
|
||||
GPy/kern/parts/prod.py
|
||||
|
||||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
|
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@ -7762,7 +7884,7 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/kern/parts/prod.py
|
||||
GPy/kern/parts/prod.py
|
||||
|
||||
* Minor changes. [Ricardo]
|
||||
|
||||
|
|
@ -8125,7 +8247,7 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Max Zwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/parameterization/param.py
|
||||
GPy/core/parameterization/param.py
|
||||
|
||||
* Fixed a couple of small params bugs. [Alan Saul]
|
||||
|
||||
|
|
@ -8140,9 +8262,9 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Max Zwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/parameterization/param.py
|
||||
GPy/core/parameterization/parameter_core.py
|
||||
GPy/core/parameterization/parameterized.py
|
||||
GPy/core/parameterization/param.py
|
||||
GPy/core/parameterization/parameter_core.py
|
||||
GPy/core/parameterization/parameterized.py
|
||||
|
||||
* Stupid error, needed to actually USE the gradients in student t... Looks like s2 of rasm's may have an extra -? dW_df == -d2logpdf_df not just d2logpdf_df? [Alan Saul]
|
||||
|
||||
|
|
@ -8227,7 +8349,7 @@
|
|||
* Merge branch 'params' of github.com:SheffieldML/GPy into params. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/sparse_gp.py
|
||||
GPy/core/sparse_gp.py
|
||||
|
||||
* Typo corrected. [Ricardo]
|
||||
|
||||
|
|
@ -8641,7 +8763,7 @@
|
|||
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/examples/classification.py
|
||||
GPy/examples/classification.py
|
||||
|
||||
* Fixed a bug in Neil's otherwise tidy hetero kernel. [James Hensman]
|
||||
|
||||
|
|
@ -8710,8 +8832,8 @@
|
|||
* Merge branch 'devel' into params. [Max Zwiessele]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/transformations.py
|
||||
GPy/kern/parts/kernpart.py
|
||||
GPy/core/transformations.py
|
||||
GPy/kern/parts/kernpart.py
|
||||
|
||||
* Merge pull request #77 from jamesmcm/devel. [James McMurray]
|
||||
|
||||
|
|
@ -8770,10 +8892,10 @@
|
|||
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/examples/regression.py
|
||||
GPy/kern/constructors.py
|
||||
GPy/testing/kernel_tests.py
|
||||
GPy/util/multioutput.py
|
||||
GPy/examples/regression.py
|
||||
GPy/kern/constructors.py
|
||||
GPy/testing/kernel_tests.py
|
||||
GPy/util/multioutput.py
|
||||
|
||||
* Other local changes. [Neil Lawrence]
|
||||
|
||||
|
|
@ -8798,15 +8920,15 @@
|
|||
* Merge branch 'linK_functions2' into devel. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/gp.py
|
||||
GPy/core/gp_base.py
|
||||
GPy/core/sparse_gp.py
|
||||
GPy/examples/regression.py
|
||||
GPy/kern/constructors.py
|
||||
GPy/kern/parts/coregionalise.py
|
||||
GPy/models/__init__.py
|
||||
GPy/models/sparse_gp_classification.py
|
||||
GPy/util/__init__.py
|
||||
GPy/core/gp.py
|
||||
GPy/core/gp_base.py
|
||||
GPy/core/sparse_gp.py
|
||||
GPy/examples/regression.py
|
||||
GPy/kern/constructors.py
|
||||
GPy/kern/parts/coregionalise.py
|
||||
GPy/models/__init__.py
|
||||
GPy/models/sparse_gp_classification.py
|
||||
GPy/util/__init__.py
|
||||
|
||||
* Useless files deleted. [Ricardo]
|
||||
|
||||
|
|
@ -9479,7 +9601,7 @@
|
|||
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/fitc.py
|
||||
GPy/core/fitc.py
|
||||
|
||||
* FITC example added. [Ricardo]
|
||||
|
||||
|
|
@ -9647,7 +9769,7 @@
|
|||
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Neil Lawrence]
|
||||
|
||||
Conflicts:
|
||||
GPy/models/GPLVM.py
|
||||
GPy/models/GPLVM.py
|
||||
|
||||
* Remove copies (they are now in visualize code ...). [Neil Lawrence]
|
||||
|
||||
|
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@ -9795,7 +9917,7 @@
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|||
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
|
||||
|
||||
Conflicts:
|
||||
GPy/models/GP.py
|
||||
GPy/models/GP.py
|
||||
|
||||
* Plot function got broken with last commit, this fixes it. [Ricardo]
|
||||
|
||||
|
|
@ -10137,7 +10259,7 @@
|
|||
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Neil Lawrence]
|
||||
|
||||
Conflicts:
|
||||
GPy/examples/dimensionality_reduction.py
|
||||
GPy/examples/dimensionality_reduction.py
|
||||
|
||||
* Minor changes. [Neil Lawrence]
|
||||
|
||||
|
|
@ -10208,8 +10330,8 @@
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|||
* Merge branch 'devel' into new_constraints. [James Hensman]
|
||||
|
||||
Conflicts:
|
||||
GPy/core/model.py
|
||||
GPy/core/parameterised.py
|
||||
GPy/core/model.py
|
||||
GPy/core/parameterised.py
|
||||
|
||||
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
|
||||
|
||||
|
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@ -10771,7 +10893,7 @@
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|||
* Merge branch 'master' of github.com:SheffieldML/GPy. [Ricardo Andrade]
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||||
|
||||
Conflicts:
|
||||
GPy/examples/__init__.py
|
||||
GPy/examples/__init__.py
|
||||
|
||||
* Working on psi cross terms. [Nicolo Fusi]
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||||
|
||||
|
|
@ -11211,7 +11333,7 @@
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|||
* Merge branch 'newGP' [James Hensman]
|
||||
|
||||
Conflicts:
|
||||
GPy/models/GP_regression.py
|
||||
GPy/models/GP_regression.py
|
||||
|
||||
* Simplified the checkgrad logic somewhat. [James Hensman]
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||||
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||||
|
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@ -11242,7 +11364,7 @@
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|||
* Merge branch 'newGP' of github.com:SheffieldML/GPy into newGP. [James Hensman]
|
||||
|
||||
Conflicts:
|
||||
GPy/likelihoods/EP.py
|
||||
GPy/likelihoods/EP.py
|
||||
|
||||
* James' debugging of the EP/GP interface. [Ricardo Andrade]
|
||||
|
||||
|
|
@ -11253,8 +11375,8 @@
|
|||
* Merge branch 'newGP' of github.com:SheffieldML/GPy into newGP. [Ricardo Andrade]
|
||||
|
||||
Conflicts:
|
||||
GPy/likelihoods/EP.py
|
||||
GPy/likelihoods/likelihood_functions.py
|
||||
GPy/likelihoods/EP.py
|
||||
GPy/likelihoods/likelihood_functions.py
|
||||
|
||||
* So many changes. [Ricardo Andrade]
|
||||
|
||||
|
|
@ -12018,3 +12140,5 @@
|
|||
* Core file. [Nicolo Fusi]
|
||||
|
||||
* Initial commit. [Nicolò Fusi]
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
__version__ = "1.9.6"
|
||||
__version__ = "1.9.8"
|
||||
|
|
|
|||
|
|
@ -23,6 +23,17 @@ class Brownian(Kern):
|
|||
|
||||
self.variance = Param('variance', variance, Logexp())
|
||||
self.link_parameters(self.variance)
|
||||
|
||||
def to_dict(self):
|
||||
"""
|
||||
Convert the object into a json serializable dictionary.
|
||||
Note: It uses the private method _save_to_input_dict of the parent.
|
||||
:return dict: json serializable dictionary containing the needed information to instantiate the object
|
||||
"""
|
||||
|
||||
input_dict = super(RBF, self)._save_to_input_dict()
|
||||
input_dict["class"] = "GPy.kern.Brownian"
|
||||
return input_dict
|
||||
|
||||
def K(self,X,X2=None):
|
||||
if X2 is None:
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -64,6 +64,11 @@ class White(Static):
|
|||
def __init__(self, input_dim, variance=1., active_dims=None, name='white'):
|
||||
super(White, self).__init__(input_dim, variance, active_dims, name)
|
||||
|
||||
def to_dict(self):
|
||||
input_dict = super(White, self)._save_to_input_dict()
|
||||
input_dict["class"] = "GPy.kern.White"
|
||||
return input_dict
|
||||
|
||||
def K(self, X, X2=None):
|
||||
if X2 is None:
|
||||
return np.eye(X.shape[0])*self.variance
|
||||
|
|
@ -102,6 +107,10 @@ class WhiteHeteroscedastic(Static):
|
|||
super(Static, self).__init__(input_dim, active_dims, name)
|
||||
self.variance = Param('variance', np.ones(num_data) * variance, Logexp())
|
||||
self.link_parameters(self.variance)
|
||||
def to_dict(self):
|
||||
input_dict = super(WhiteHeteroscedastic, self)._save_to_input_dict()
|
||||
input_dict["class"] = "GPy.kern.WhiteHeteroscedastic"
|
||||
return input_dict
|
||||
|
||||
def Kdiag(self, X):
|
||||
if X.shape[0] == self.variance.shape[0]:
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -6,6 +6,8 @@ cimport numpy as np
|
|||
from cython.parallel import prange
|
||||
cimport cython
|
||||
|
||||
np.import_array()
|
||||
|
||||
ctypedef np.float64_t DTYPE_t
|
||||
|
||||
cdef extern from "stationary_utils.h":
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -493,7 +493,7 @@ cdef class AQcompute_batch_Cython(Q_handling_Cython):
|
|||
U,S,Vh = self.Q_svd_dict[matrix_index]
|
||||
|
||||
square_root = U * np.sqrt(S)
|
||||
self.Q_suqare_root_dict[matrix_index] = square_root
|
||||
self.Q_square_root_dict[matrix_index] = square_root
|
||||
|
||||
return square_root
|
||||
|
||||
|
|
|
|||
|
|
@ -356,7 +356,7 @@ def x_frame1D(X,plot_limits=None,resolution=None):
|
|||
else:
|
||||
raise ValueError("Bad limits for plotting")
|
||||
|
||||
Xnew = np.linspace(xmin,xmax,resolution or 200)[:,None]
|
||||
Xnew = np.linspace(float(xmin),float(xmax),int(resolution) or 200)[:,None]
|
||||
return Xnew, xmin, xmax
|
||||
|
||||
def x_frame2D(X,plot_limits=None,resolution=None):
|
||||
|
|
|
|||
|
|
@ -6,7 +6,6 @@ from . import linalg
|
|||
from . import misc
|
||||
from . import squashers
|
||||
from . import warping_functions
|
||||
from . import datasets
|
||||
from . import mocap
|
||||
from . import decorators
|
||||
from . import classification
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -9,10 +9,12 @@ from cython.parallel import prange, parallel
|
|||
cimport numpy as np
|
||||
cimport scipy.linalg.cython_blas as cblas
|
||||
|
||||
np.import_array()
|
||||
|
||||
def flat_to_triang(double[:, :] flat, int M):
|
||||
"""take a matrix N x D and return a D X M x M array where
|
||||
|
||||
N = M(M+1)/2
|
||||
N = M(M+1)//2
|
||||
|
||||
the lower triangluar portion of the d'th slice of the result is filled by the d'th column of flat.
|
||||
"""
|
||||
|
|
@ -33,7 +35,7 @@ def flat_to_triang(double[:, :] flat, int M):
|
|||
def triang_to_flat(double[:, :, :] L):
|
||||
cdef int D = L.shape[0]
|
||||
cdef int M = L.shape[1]
|
||||
cdef int N = M*(M+1)/2
|
||||
cdef int N = M*(M+1)//2
|
||||
cdef int count = 0
|
||||
cdef double[:, ::1] flat = np.empty((N, D))
|
||||
cdef int d, m, mm
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
10
README.md
10
README.md
|
|
@ -99,6 +99,16 @@ the [anaconda python distribution](http://continuum.io/downloads).
|
|||
With anaconda you can install GPy by the following:
|
||||
|
||||
conda update scipy
|
||||
|
||||
Then potentially try,
|
||||
|
||||
sudo apt-get update
|
||||
sudo apt-get install python3-dev
|
||||
sudo apt-get install build-essential
|
||||
conda update anaconda
|
||||
|
||||
And finally,
|
||||
|
||||
pip install gpy
|
||||
|
||||
We've also had luck with [enthought](http://www.enthought.com). Install scipy 0.16 (or later)
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@ environment:
|
|||
secure: 8/ZjXFwtd1S7ixd7PJOpptupKKEDhm2da/q3unabJ00=
|
||||
COVERALLS_REPO_TOKEN:
|
||||
secure: d3Luic/ESkGaWnZrvWZTKrzO+xaVwJWaRCEP0F+K/9DQGPSRZsJ/Du5g3s4XF+tS
|
||||
gpy_version: 1.9.6
|
||||
gpy_version: 1.9.8
|
||||
matrix:
|
||||
- PYTHON_VERSION: 2.7
|
||||
MINICONDA: C:\Miniconda-x64
|
||||
|
|
@ -11,8 +11,8 @@ environment:
|
|||
MINICONDA: C:\Miniconda35-x64
|
||||
- PYTHON_VERSION: 3.6
|
||||
MINICONDA: C:\Miniconda36-x64
|
||||
# - PYTHON_VERSION: 3.7
|
||||
# MINICONDA: C:\Miniconda36-x64
|
||||
- PYTHON_VERSION: 3.7
|
||||
MINICONDA: C:\Miniconda36-x64
|
||||
|
||||
#configuration:
|
||||
# - Debug
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
[bumpversion]
|
||||
current_version = 1.9.6
|
||||
current_version = 1.9.8
|
||||
tag = True
|
||||
commit = True
|
||||
|
||||
|
|
@ -12,3 +12,4 @@ upload-dir = doc/build/html
|
|||
|
||||
[medatdata]
|
||||
description-file = README.rst
|
||||
|
||||
|
|
|
|||
10
setup.py
10
setup.py
|
|
@ -84,28 +84,28 @@ try:
|
|||
import numpy as np
|
||||
|
||||
ext_mods = [Extension(name='GPy.kern.src.stationary_cython',
|
||||
sources=['GPy/kern/src/stationary_cython.c',
|
||||
sources=['GPy/kern/src/stationary_cython.pyx',
|
||||
'GPy/kern/src/stationary_utils.c'],
|
||||
include_dirs=[np.get_include(), '.'],
|
||||
extra_compile_args=compile_flags,
|
||||
extra_link_args=link_args),
|
||||
Extension(name='GPy.util.choleskies_cython',
|
||||
sources=['GPy/util/choleskies_cython.c'],
|
||||
sources=['GPy/util/choleskies_cython.pyx'],
|
||||
include_dirs=[np.get_include(), '.'],
|
||||
extra_link_args=link_args,
|
||||
extra_compile_args=compile_flags),
|
||||
Extension(name='GPy.util.linalg_cython',
|
||||
sources=['GPy/util/linalg_cython.c'],
|
||||
sources=['GPy/util/linalg_cython.pyx'],
|
||||
include_dirs=[np.get_include(), '.'],
|
||||
extra_compile_args=compile_flags,
|
||||
extra_link_args=link_args),
|
||||
Extension(name='GPy.kern.src.coregionalize_cython',
|
||||
sources=['GPy/kern/src/coregionalize_cython.c'],
|
||||
sources=['GPy/kern/src/coregionalize_cython.pyx'],
|
||||
include_dirs=[np.get_include(), '.'],
|
||||
extra_compile_args=compile_flags,
|
||||
extra_link_args=link_args),
|
||||
Extension(name='GPy.models.state_space_cython',
|
||||
sources=['GPy/models/state_space_cython.c'],
|
||||
sources=['GPy/models/state_space_cython.pyx'],
|
||||
include_dirs=[np.get_include(), '.'],
|
||||
extra_compile_args=compile_flags,
|
||||
extra_link_args=link_args)]
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue