{"action":"created","issue":{"url":"https://api.github.com/repos/SheffieldML/GPy/issues/229","labels_url":"https://api.github.com/repos/SheffieldML/GPy/issues/229/labels{/name}","comments_url":"https://api.github.com/repos/SheffieldML/GPy/issues/229/comments","events_url":"https://api.github.com/repos/SheffieldML/GPy/issues/229/events","html_url":"https://github.com/SheffieldML/GPy/pull/229","id":105410148,"number":229,"title":"Devel","user":{"login":"mzwiessele","id":1563689,"avatar_url":"https://avatars.githubusercontent.com/u/1563689?v=3","gravatar_id":"","url":"https://api.github.com/users/mzwiessele","html_url":"https://github.com/mzwiessele","followers_url":"https://api.github.com/users/mzwiessele/followers","following_url":"https://api.github.com/users/mzwiessele/following{/other_user}","gists_url":"https://api.github.com/users/mzwiessele/gists{/gist_id}","starred_url":"https://api.github.com/users/mzwiessele/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mzwiessele/subscriptions","organizations_url":"https://api.github.com/users/mzwiessele/orgs","repos_url":"https://api.github.com/users/mzwiessele/repos","events_url":"https://api.github.com/users/mzwiessele/events{/privacy}","received_events_url":"https://api.github.com/users/mzwiessele/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-09-08T15:49:20Z","updated_at":"2015-09-08T15:59:34Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/SheffieldML/GPy/pulls/229","html_url":"https://github.com/SheffieldML/GPy/pull/229","diff_url":"https://github.com/SheffieldML/GPy/pull/229.diff","patch_url":"https://github.com/SheffieldML/GPy/pull/229.patch"},"body":"Creating 0.8 release through pull request"},"comment":{"url":"https://api.github.com/repos/SheffieldML/GPy/issues/comments/138609640","html_url":"https://github.com/SheffieldML/GPy/pull/229#issuecomment-138609640","issue_url":"https://api.github.com/repos/SheffieldML/GPy/issues/229","id":138609640,"user":{"login":"lawrennd","id":133722,"avatar_url":"https://avatars.githubusercontent.com/u/133722?v=3","gravatar_id":"","url":"https://api.github.com/users/lawrennd","html_url":"https://github.com/lawrennd","followers_url":"https://api.github.com/users/lawrennd/followers","following_url":"https://api.github.com/users/lawrennd/following{/other_user}","gists_url":"https://api.github.com/users/lawrennd/gists{/gist_id}","starred_url":"https://api.github.com/users/lawrennd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lawrennd/subscriptions","organizations_url":"https://api.github.com/users/lawrennd/orgs","repos_url":"https://api.github.com/users/lawrennd/repos","events_url":"https://api.github.com/users/lawrennd/events{/privacy}","received_events_url":"https://api.github.com/users/lawrennd/received_events","type":"User","site_admin":false},"created_at":"2015-09-08T15:59:34Z","updated_at":"2015-09-08T15:59:34Z","body":"Wow what a list of changes great job *everyone*. Thanks so much to all, but\nparticularly Max and Mike for leading the process. Also James for chasing\ndown so many of the outstanding issues.\n\nAs from 0.8 we will begin making more regular minor releases. We will form\na developers' meeting, I suspect monthly initially. Then perhaps minor\nreleases to GPy bimonthly.\n\nWatch this space for more details, they will be hammered out when Mike and\nMax have time to catch breath. We'll get in touch directly with some of the\nmore high volume commiters with details.\n\nNeil\nOn 8 Sep 2015 16:49, \"Max Zwiessele\" <notifications@github.com> wrote:\n\n> Creating 0.8 release through pull request\n> ------------------------------\n> You can view, comment on, or merge this pull request online at:\n>\n>   https://github.com/SheffieldML/GPy/pull/229\n> Commit Summary\n>\n>    - [predict] documentation\n>    - [predict] documentation\n>    - [cython import] error notices where it happens\n>    - [opt messages] show dd/hh:mm:ss.ms\n>    - [opt messages] show DDdHHhMMmSSsMS\n>    - svgp, more c-ordering\n>    - change the behavior the optimize_restarts to keep the original model\n>    parameters for the firt run\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - omp for gradients_X\n>    - Merge branch 'devel' into reorder_choleskies\n>    - interim svgp commit\n>    - svgp working with reordered chols\n>    - Merge branch 'devel' of github.com:/sheffieldml/GPy into devel\n>    - Merge branch 'reorder_choleskies' into devel\n>    - small bug in cython tests\n>    - prevent the predicted variance to be negative\n>    - start implement ICP for ssgplvm\n>    - svgp bugfix\n>    - some cython improvments for stationary kerns\n>    - minor bugfix in mlp kernel\n>    - Merge branch 'devel' of github.com:/sheffieldml/gpy into devel\n>    - [param] added multilevel indexing note to doc\n>    - [ssgplvm] group spike\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [ssgplvm] implement IBP prior\n>    - Added option for plotting with SVGP\n>    - [ssmrd] implement with IBP prior\n>    - Reshaped log predictive density to have D outputs\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - Updated plotting\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - minor bugfix in raw_predict with full_cov for sparseGP\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - added log jacobian transofms for Exponent, Logexp\n>    - [ssgplvm] change the default gamma interval\n>    - allow to set color for the skeleton visualization\n>    - jacobian bugfix\n>    - Merge branch 'devel' of github.com:/sheffieldml/gpy into devel\n>    - Jacobians should not be computed only for transforms\n>    - Jacobians should not be computed only for transforms\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - parallelizing backprop of cholesky\n>    - fiddling with cholesky backprop\n>    - lots of work on cython choleskies\n>    - sqrt pi term was missing in variational expectations\n>    - allowing set initial noise variance for GPRegression\n>    - Python 3 fixes\n>    - Passing on y_metadata\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - some correction for ibp ssgplvm\n>    - [verbose opt] verbose needed clear after finish push through\n>    - [parameterized] merge in jacobian for priors?\n>    - [plotting] parameterized.values\n>    - [inference] minibatch inference needed polishing\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - Cache some values\n>    - ENH: Adding standard periodic kernel\n>    - TEST: Adding test for periodic kernel\n>    - TEST: Making test for the Standard Periodic Kernel similar to other\n>    kernel tests.\n>    - generalized the variatinoal Gaussian approximatino revisited code\n>    for any likelihood\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Change crescent data to optimize with .optimize()\n>    - Passing metadata\n>    - Changed quantile computation via sampling and added fallback for\n>    predictive mean and variance if conditional mean and variance are not\n>    implemented yet\n>    - Fixed model test\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - improve the documentation of infer_newX\n>    - fix DGPLVM prior\n>    - changes\n>    - merge the changes\n>    - [bgplvm] technical new stuff\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - The bug fix for the cblas.h problem in Mac os x\n>    - allow Y to be uncertain\n>    - bug fix: the name of parameterable object is not removed when\n>    unlinking\n>    - Python 3 fixes\n>    - rbf psi-statistics speed improvement\n>    - fixed SVGP tests\n>    - Merge pull request #212 from mikecroucher/devel\n>    - fixed strange bug. In python 3, numbers startin 0 are octal.\n>    - merging. conflict in relative import styles\n>    - Merge branch 'tjhgit-devel' into devel\n>    - fixed conflict in plotting\n>    - fixed relative import in spline\n>    - caught warnings in misc_tests\n>    - removed randomness from inference tests by setting np.seed\n>    - tidied model_tests\n>    - change the default name of sparse_gp_mpi class\n>    - fixed a plotting bug\n>    - Merge branch 'devel' of github.com:/sheffieldml/GPy into devel\n>    - fixing qualtile code for some likelhoods\n>    - Merge pull request #183 from AlexGrig/std_periodic_kernel\n>    - another relative import (py3) bug\n>    - ENH: fixed up BCGPLVM to work with new framework\n>    - ENH: implementing the Cholesky backpropagation through Scipy's BLAS\n>    - FIX: transforming the indexing to 2D\n>    - FIX: ensuring contiguity of the buffers for BLAS call and returning\n>    a Numpy array\n>    - Merge branch 'devel-cythonchol' of git://github.com/Dapid/GPy into\n>    Dapid-devel-cythonchol\n>    - adding new test for cholesky backprop\n>    - Merge branch 'devel' into Dapid-devel-cythonchol\n>    - ENH: various Cython enhancements, mostly releasing the GIL when not\n>    needed\n>    - minor corrections :)\n>    - reenabling gil\n>    - running cython\n>    - Merge branch 'Dapid-devel-cythonchol' into devel\n>    - tidied setup.py\n>    - Merge pull request #216 from Dapid/devel-cython_update\n>    - tidied link_fn tests\n>    - Merge branch 'devel' of github.com:/sheffieldml/GPy into devel\n>    - improve the stability of parallel inference code\n>    - minor bugfixes in plotting: quantiles are now computed using\n>    predict_kw\n>    - the Opper-Archambeau method is now implemented as an inference\n>    method in the GPy style\n>    - Added testing of variational expectations, analytic vs numeric, and\n>    gradient checks\n>    - adding var_gauss.py\n>    - Added fallback for non-identity link function for Gaussian\n>    variational expectations\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - Added variational expectation tests updates\n>    - Updated travis for 0.16 scipy\n>    - Removed installation conflict\n>    - sqrt(pi) term fix in Bernoulli\n>    - Merge branch 'devel' of github.com:/sheffieldml/gpy into devel\n>    - Fixed laplace seed, added debugging for misc tests\n>    - Trying to make travis print warnings\n>    - gradients w.r.t. kappa corrected\n>    - psi-statistics for any kernels via Gaussian quadrature\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - add missing file\n>    - FIX: now Scipy 0.16 is required, removing fixes for older versions.\n>    Accessing blas through the scipy interface\n>    - Fixing confussion between lapack and ctypes interfaces\n>    - Fixing the blas arguments for DSYRK\n>    - Fixed array2string bug for N > 1000 default printing\n>    - adding a white kernel to a sparseGP test for stability\n>    - fixed random seed for kronecker tests\n>    - Optimizing missing data model, needs tidying but now much faster\n>    - add the regression benchmark\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - remove the old housing benchmark\n>    - Tidied but broken\n>    - add MRD for regression benchmark\n>    - Made sparse gp work again\n>    - Gradients for X seem to match\n>    - Checking kerngrads full_value\n>    - Removed comment\n>    - [heteroscedastic gauss] Implemented Heteroscedastic Guassian Lik\n>    with @ric70x7\n>    - [heteroscedastic gauss] Implemented Heteroscedastic Guassian Lik\n>    with @ric70x7\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - passing psi statistics\n>    - Try calculating dL_dpsi1*psi1 individually for each dimension as we\n>    go along\n>    - corrected caching for psi derivatives\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - ensuring the shape of the mean vector at predict time fixes bug in\n>    EP prediction\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - Merge branch 'devel' into missing_opt\n>    - Reindented, did some profiling which looks promising\n>    - [core] updating system, security branching\n>    - Merge branch 'updates' into devel\n>    - Model uses the new HeteroscedasticGaussian likelihood\n>    - New likelihood: HeteroscedasticGaussian\n>    - Change in _diag_ufunc with @mzwiessele\n>    - Note added to the docs\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [merge]\n>    - [hetnoise] import correction\n>    - [magnification] mostly plotting and some model corrections for\n>    _predictive_variable\n>    - Merge pull request #219 from Dapid/fix_209\n>    - New function to plot just the errorbars of the training data\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [magnification] plot_magnification expanded\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [magnification] added static kernel support and faster derivative\n>    computations\n>    - [magnification] static corrections\n>    - Small edits for linear kernel\n>    - [add] renamed>sum\n>    - add util.parallel into import\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - FIX: missing compatibility Py2/3\n>    - Shape of heteroscedastic variance corrected\n>    - gperrors color as parameter\n>    - errorbars fixed\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Merge pull request #224 from Dapid/fix_print\n>    - [spgp minibatch] added new routine for psi NxMxM, much faster,\n>    little bigger mem footbprint\n>    - [merge] for spgp minibatch and psi NxMxM\n>    - [spgp] minibatch testing\n>    - [mrd] fixes for updates on psi2\n>    - [psi2] NxMxM fixes for the add kernel\n>    - add psi-statistics test\n>    - fall back to the old psicomp interfacegit status!\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [coverage] added normalizer tests\n>    - [coverage] test predict sparse gp\n>    - [coverage] script to create coverage output html\n>    - [spgp minibatch] linear calls the right psicomps and add kernel\n>    - Cleanup unused imports\n>    - [psi2n] added psi2n for static kernels\n>    - slightly improved computation for var_Gauss method\n>    - [psi2n] Liner psi2 statistics now implemented for separate n\n>    - [setxy] always run the update after updating X and Y\n>    - [core] visited as propery\n>    - [caching] different error\n>    - Revert \"[caching] different error\"\n>    - Revert \"[core] visited as propery\"\n>    - [pickling] pickle error\n>    - [empty space] literally : )\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [MRD] fixed mrd for new structure\n>    - allow cache supporting boolean and integers\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Merge pull request #227 from Dapid/clean_imports\n>    - unify the interface of psicomp, but the psi2n of linear kernel and\n>    gaussian qradrature still needs to be done.\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - new implementation for mlp kernel (speed improvemd)\n>    - fix linear kernel with NxMxM psi2\n>    - Automatic fallback to Numpy if Cython modules not available\n>    - Fixes Cython compilation on Mac OS X\n>    - speed tuning for mlp kernel and gauss qudrature for psi-statistics\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Python 3 fixes\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - [coverage] tests for coverage increase\n>    - [mean func] added in GPRegression\n>    - [predict] using gp predict in sparse gp and predictive variable\n>    - git pushMerge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Python 3 fixes\n>    - Fixed typos\n>    - Used scipy.log1p since it gives more consistent results\n>    cross-platform\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - changed gpu interface for mpi\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Switched to scipy.special.log1p@\n>    - Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel\n>    - Used scipy.log1p since it gives more consistent results\n>    cross-platform\n>    - [more coverage] and predictive var fixes\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - optimize util for mpi\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [licensing] replaced licensing with BSD, and erfcx\n>    - git pushMerge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Fixed for Python 3\n>    - [doc] some changes to the doc, using mathjax some additions in math\n>    - Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - Update README.md\n>    - [testing]\n>    - git Merge branch 'devel' of github.com:SheffieldML/GPy into devel\n>    - [readthedocs] forcing readthedocs into not failing\n>    - [readthedocs] forcing readthedocs into not failing\n>    - [readthedocs] forcing readthedocs into not failing\n>    - [test] adding some more tests for coverage\n>    - [readthedocs] forcing readthedocs into not failing\n>    - [readthedocs] forcing readthedocs into not failing\n>\n> File Changes\n>\n>    - *M* .travis.yml\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-0> (5)\n>    - *M* AUTHORS.txt\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-1> (1)\n>    - *M* GPy/__init__.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-2> (26)\n>    - *M* GPy/core/__init__.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-3> (15)\n>    - *M* GPy/core/gp.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-4> (392)\n>    - *M* GPy/core/mapping.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-5> (116)\n>    - *M* GPy/core/model.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-6> (93)\n>    - *M* GPy/core/parameterization/__init__.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-7> (4)\n>    - *M* GPy/core/parameterization/index_operations.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-8> (67)\n>    - *M* GPy/core/parameterization/lists_and_dicts.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-9> (4)\n>    - *M* GPy/core/parameterization/observable.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-10> (25)\n>    - *M* GPy/core/parameterization/observable_array.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-11> (6)\n>    - *M* GPy/core/parameterization/param.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-12> (54)\n>    - *M* GPy/core/parameterization/parameter_core.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-13> (129)\n>    - *M* GPy/core/parameterization/parameterized.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-14> (56)\n>    - *M* GPy/core/parameterization/priors.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-15> (516)\n>    - *M* GPy/core/parameterization/ties_and_remappings.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-16> (18)\n>    - *M* GPy/core/parameterization/transformations.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-17> (114)\n>    - *M* GPy/core/parameterization/updateable.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-18> (17)\n>    - *M* GPy/core/parameterization/variational.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-19> (98)\n>    - *M* GPy/core/sparse_gp.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-20> (119)\n>    - *M* GPy/core/sparse_gp_mpi.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-21> (6)\n>    - *A* GPy/core/svgp.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-22> (105)\n>    - *M* GPy/core/symbolic.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-23> (2)\n>    - *A* GPy/core/verbose_optimization.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-24> (185)\n>    - *M* GPy/defaults.cfg\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-25> (3)\n>    - 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*M* MANIFEST.in\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-190> (3)\n>    - *M* README.md\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-191> (67)\n>    - *A* benchmarks/regression/evaluation.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-192> (21)\n>    - *A* benchmarks/regression/methods.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-193> (109)\n>    - *A* benchmarks/regression/outputs.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-194> (64)\n>    - *A* benchmarks/regression/run.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-195> (53)\n>    - *A* benchmarks/regression/tasks.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-196> (86)\n>    - *M* doc/conf.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-197> (14)\n>    - *M* doc/index.rst\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-198> (2)\n>    - *M* doc/log.txt\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-199> (226)\n>    - *M* setup.py\n>    <https://github.com/SheffieldML/GPy/pull/229/files#diff-200> (42)\n>\n> Patch Links:\n>\n>    - https://github.com/SheffieldML/GPy/pull/229.patch\n>    - https://github.com/SheffieldML/GPy/pull/229.diff\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/SheffieldML/GPy/pull/229>.\n>\n"}}