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b13937d Changes for tf0.12 (#307) * Changes for tf0.12. * Modified tests as well, updated readme & version. * Update .travis.yml 11 January 2017, 09:06 UTC
2049274 adding overflow check and bugfix. (#303) 20 December 2016, 15:02 UTC
05042f4 Sgpr notes (#296) * Small corrections to SGPR notes. * adding missing equals signs. 14 December 2016, 13:45 UTC
851fac3 minor updates to hmc.py (#293) 05 December 2016, 20:43 UTC
7ae7fff fix minor bug in MultiClass when passing invlink (#291) 05 December 2016, 09:28 UTC
9366211 Improve test coverage for stochastic gradients with tf optimizer. (#287) * Adding sequential generation to minibatch class. * Test minibatch data. * Correction on basis of test. * Pulling out sequence generation. * Building up svgp regression test. * Pulling out minibatch functionality into new python file. * adding test of sampler logic. 30 November 2016, 08:09 UTC
262f652 Feed dict needs to be updated on each iteration. (#285) 26 November 2016, 15:06 UTC
d53a9c6 Paramlist constructor bugfix (#282) * changed default argument behaviour for paramlist * tests to cover paramlist constructor 26 November 2016, 12:43 UTC
e6579d4 added test for multiple Y columns. Fix in SGPR and GPRFITC (#283) 25 November 2016, 17:18 UTC
3ab7139 fixing bug #277, copy error in mean function constructors (#278) * fixing bug #277, copy error in mean functino constructors * improved default logic for mean fnction constructors 24 November 2016, 14:44 UTC
1b7b2df Merge pull request #276 from GPflow/update-travis Update travis 24 November 2016, 10:46 UTC
c0bfa30 Merge branch 'master' into update-travis 24 November 2016, 10:29 UTC
876a511 travis now uses relase version of tf 24 November 2016, 10:12 UTC
1de5083 docs now use python 3.4 (#275) 24 November 2016, 09:59 UTC
6f036af trying puthon 3.4 24 November 2016, 09:40 UTC
db38323 Kernel expectations (#195) This squash-commit contains a large volume of work by @markvdw and @alexisboukouvalas. I'm keeping all of the commit history here for posterity. Interested viewers can see some discussion on github, under pull request #195. * Initial code for new kernel expectations. - RBF done. - Added another transformation in etransforms.py. * first step to merge gplvm and kernexp approaches * Added kernel expectations of linear, and eKxz for RBF. - NB: Linear still need to be tested better. - Todo: exKxz for linear. * Added multidimensional quadrature in `Kern` base class for kernel expectations. - Replaced monte carlo tests with more reliable quadrature tests. - Added exKxz for `Linear` kernel * testing new ekernels code, starting on active dimensions, further testing needed as well as modifying Bayesian GPLVM code * Linear and Polynomial kernels did not respect active_dims properly in Kdiag. - Added slice call to Linear.Kdiag - Fixed TestSlice to test more kernels. - Fxied TestSlice to have the correct inputdim. * Begin work on sum kernel, smoothing out active_dims for ekernels. * Fixed `input_dim` in `test_kerns.py`. Added assertion. * kernexp quadrature now works with `active_dims`. - exKzx which doesn't work now raises an error from TensorFlow. - Various other assertions. * Better deduction of `input_dim` for `kernels.Combination`. * Small fix of test. * Fixed issue of KzxKxz in Add kernel. Solution checks for diagonal q(X) and performs quadrature on the covariance of KzxKxz if not diagonal. * GPLVM now works with new kernel expectation code. - Added a new DiagMatrix transform. - Removed legacy code. - Modified GPLVM to accept full covariance matrices. * Fixing a small error in DiagMatrix transform. * Added warnings. * Removed etransforms code. BlockTriDiagonalTransform is now only used in tests. * Prevent `TridiagonalBlockRep` from being tested as a `Transform`. * improvements to DiagonalMatrix transform * improved testing of kernel slice * update test to use kernels * `ekernels.RBF` ARD bug fixed. * Increased test coverage. * Increased test coverage. * docstring for gplvm, removed unused variable in ekernels * testing composite kernels in gplvm * Added Prod to `ekernels.py`. * Fixed usage of `tf.gather_nd`, which does not have a gradient in `_slice_cov()`. * add GPLVM notebook, increase testing to include Prod kernels, add documentation stub, fix bibliography * improve GPLVM notebook with working example * Fixed bug that `X_var` in `BayesianGPLVM` gets slightly different values. * Quadrature can be switched off, plus the appropriate checks. * Kernel expectations now accept 2D variances. * Fix to test. * Reworked quadrature code in Add in anticipation of adding exact expectations for certain pairs of kernels. * Added Linear + Add cross terms for overlapping active_dims. * Initial try for extra test for `ekernels.Add` cross terms. * `_slice_cov` now again compatible with numpy arrays. * Requested code reviews. 23 November 2016, 18:31 UTC
419c43b Merge pull request #273 from GPflow/jameshensman-readme-patch point to tensorflow 0.11 in readme (not 0.10) 21 November 2016, 10:45 UTC
f2883d5 Merge branch 'master' into jameshensman-readme-patch 21 November 2016, 09:08 UTC
9999cc4 point to tensorflow 0.11 in readme (not 0.10) 21 November 2016, 09:07 UTC
efbea03 Patch setattr (#272) * Patch for #269 * Replacement of Parameterized now raises _needs_recompile flag. * Fix typo 20 November 2016, 08:19 UTC
4005d83 Update kernels.ipynb (#271) Corrected a couple of typos in the text. 18 November 2016, 15:04 UTC
9de24ca Patch for #269 (#270) Fix bug in equality comparison: fails on some systems due to floating point error. 17 November 2016, 12:33 UTC
3f9c248 Bibtex docs (#263) * Adding the GPflow bibtex. * Tweaking bibtex * Tweaking Readme order. 09 November 2016, 14:12 UTC
c84bc39 Merge pull request #145 from GPflow/multi-likelihood Multi likelihood 07 November 2016, 16:10 UTC
7131e7f Merge branch 'master' into multi-likelihood 07 November 2016, 13:21 UTC
a1c5340 add fn to gte the length of a paramlist (#220) * add fn to ge the length of a paramlist * a very simple test for the length of a paramlist 04 November 2016, 17:16 UTC
d0b3a7e small update to meanfunction tests 04 November 2016, 14:51 UTC
2500a54 Merge branch 'master' into multi-likelihood 04 November 2016, 14:23 UTC
2a755d5 Incrementing minor version number to 0.3.4 (#262) * Incrementing minor version number. * Correcting typo. 04 November 2016, 14:23 UTC
7ee159d Merge pull request #261 from GPflow/autoflow-fix Autoflow fix 04 November 2016, 13:38 UTC
bbb0c6c Merge branch 'master' into autoflow-fix 04 November 2016, 10:37 UTC
dd4727f Better deduction of `input_dim` for `kernels.Combination` (#258) * Better deduction of `input_dim` for `kernels.Combination`. * Fix small off-by-one-error k.active_dims contain indices, and we want number of columns. 04 November 2016, 08:24 UTC
7bdb7f8 minor edits to tests for new update_feed_dict functionality 03 November 2016, 22:09 UTC
834290e small change to the order of operations 03 November 2016, 21:04 UTC
7cacea5 Merge branch 'autoflow-fix' of github.com:gpflow/GPflow into autoflow-fix 03 November 2016, 21:00 UTC
5eea975 minor bugfix 03 November 2016, 21:00 UTC
a69f023 Merge branch 'master' into autoflow-fix 03 November 2016, 20:55 UTC
597eb6e changes to the get_feed_dict mechanism 03 November 2016, 20:49 UTC
d7dc9e8 aadint test to cover bad AutoFlow computations 03 November 2016, 20:11 UTC
377a45b Updates to readme file. (#259) 03 November 2016, 20:01 UTC
7ff195a bugfix in vgp (for multiple concurrent Y) 03 November 2016, 14:24 UTC
f3ecd45 Merge branch 'multi-likelihood' of github.com:gpflow/GPflow into multi-likelihood 03 November 2016, 14:00 UTC
ac6f42e Merge remote-tracking branch 'origin/master' into multi-likelihood 03 November 2016, 14:00 UTC
f1ec927 Merge branch 'master' into multi-likelihood 03 November 2016, 13:59 UTC
8e1d014 Correcting a typo in readme. (#255) 03 November 2016, 11:39 UTC
55e5bbe Updating list of contributors (#254) * Updating list of contributors. * Adding Ivo. 03 November 2016, 11:18 UTC
d5addce active_dims fix in Kdiag (#253) * Linear and Polynomial kernels did not respect active_dims properly in Kdiag. - Added slice call to Linear.Kdiag - Fixed TestSlice to test more kernels. - Fxied TestSlice to have the correct inputdim. * Fixed `input_dim` in `test_kerns.py`. Added assertion. 02 November 2016, 12:33 UTC
7801f75 merging test_likelihoods.py 01 November 2016, 17:36 UTC
82af806 Merge branch 'master' into multi-likelihood 01 November 2016, 14:06 UTC
3ba0758 merging 01 November 2016, 14:05 UTC
f66dda5 improvements to doctring of kernels regarding slices (#252) 01 November 2016, 12:03 UTC
4311448 improvements to setup.py (#251) 01 November 2016, 11:07 UTC
94a756d make sure log jacobian is computed even for fixed variables (#248) 01 November 2016, 10:47 UTC
97bda5a Fix matpackops compilation with gcc 6 (#222) 31 October 2016, 18:06 UTC
b8b91e0 Merge pull request #239 from GPflow/graphing Graphing 31 October 2016, 09:54 UTC
70eae34 Merge branch 'master' into graphing 28 October 2016, 15:58 UTC
b89794d Merge pull request #245 from GPflow/version_fix fixing tf version in setup.py 28 October 2016, 13:09 UTC
23bc64c fixing tf version in setup.py 28 October 2016, 12:51 UTC
bbd58e5 Merge branch 'master' into graphing 27 October 2016, 15:20 UTC
512007d v0.3.3 paper submission. (#243) 27 October 2016, 15:06 UTC
66508ff Merge pull request #242 from GPflow/doc_update updating tf version in docs_require 27 October 2016, 14:44 UTC
3fd0fcf Merge branch 'master' into doc_update 27 October 2016, 14:28 UTC
fbde5b3 Adding Apache license to all testing files. (#240) 27 October 2016, 14:27 UTC
ee85279 Merge pull request #241 from GPflow/tidy_notebooks tidying notebook files 27 October 2016, 14:12 UTC
d3f62da updating tf version in docs_require 27 October 2016, 14:09 UTC
12d2c80 moving notebooks around 27 October 2016, 14:00 UTC
5c523ec small fixes to scope tests 26 October 2016, 21:56 UTC
f08193d fixes in test_variational 26 October 2016, 21:24 UTC
e5b4571 fixing build_prior_KL test 26 October 2016, 21:15 UTC
cf4b659 pep8ifying test_variational 26 October 2016, 21:03 UTC
27addff improvements to model picklability 26 October 2016, 20:27 UTC
a6b6b42 model.py: make _objective functn on its own graph 26 October 2016, 20:15 UTC
5a2ea6e some small changes to get placeholders off the default graph 26 October 2016, 20:02 UTC
1ebcba3 simplification of Logistic transform 26 October 2016, 19:51 UTC
ef93b12 minor fixes in testDataHolder 26 October 2016, 19:26 UTC
4cef013 chanegs to the way fixed placeholder work Fixed variables are treated as placeholders. In this change, the placeholder is created on the call to make_tf_array, rather than at the moment that the fixed bool is set. This lets the placeholder be created inside the graph context. 26 October 2016, 19:15 UTC
f5b94dd Keep AutoFlow computations off the default graph The Autoflow function now makes its own graph for each autoflow in the model. Some extra tests in test_AutoFlow are added to make sure that it works with dataholders. The dataHolder class has changed a little: it's included in make_tf_array now, so that the placeholders can be made inside the Autoflow graph: before, all placeholders were on the default graph. 26 October 2016, 19:10 UTC
b811d4f Merge pull request #238 from GPflow/versionupdate3.2 Versionupdate3.2 24 October 2016, 14:39 UTC
6d4340a incrementing version number in docs 24 October 2016, 14:17 UTC
815f799 incrementing version number 24 October 2016, 14:17 UTC
f8568f0 Merge pull request #237 from GPflow/tf11 Tf11 24 October 2016, 14:06 UTC
aab0dc0 Merge branch 'tf11' of github.com:gpflow/GPflow into tf11 24 October 2016, 13:37 UTC
fac828a edits to travis file for tf11 24 October 2016, 13:37 UTC
2c99663 setup.py: adding pandas as requirement, updating to tf11rc1 24 October 2016, 12:24 UTC
35b07ef using tf 11 in readme 24 October 2016, 12:23 UTC
f6decf3 Merge branch 'master' into tf11 22 October 2016, 07:23 UTC
c51f17a Merge branch 'master' of github.com:gpflow/GPflow 22 October 2016, 07:23 UTC
b4b42a9 adding gpflowrc to the manifest file (#233) 22 October 2016, 07:23 UTC
c2dfd94 adding gpflowrc to the manifest file 21 October 2016, 14:39 UTC
e20a789 using tf11rc0 until the release of 0.11 21 October 2016, 14:38 UTC
9b5b5f4 Merge pull request #124 from GPflow/ordinal Likelihood for Ordinal regression 16 October 2016, 19:41 UTC
51308f9 slight change to logic in tests 16 October 2016, 15:31 UTC
9e8e6cf slightly tidier likelihood tests 16 October 2016, 14:48 UTC
c51dead minor fixes for ordinal notebook, ggplot style after inline, typos 16 October 2016, 10:01 UTC
cea36c1 manual merge 16 October 2016, 09:54 UTC
957742a Merge branch 'master' into ordinal 16 October 2016, 09:16 UTC
6af7095 Fix links to the example notebooks (#221) 10 October 2016, 09:21 UTC
3778ae9 Update README.md (#218) 04 October 2016, 08:07 UTC
46e9318 Added return statements in vgp._compile(). (#219) 03 October 2016, 14:32 UTC
01c6e27 Fixes for TF 0.11 (#217) * Fixed some batch_ methods for TF 0.11 * The Tensor ops class has moved in TF 0.11 03 October 2016, 12:57 UTC
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