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Revision Author Date Message Commit Date
e24fd81 Start multioutput likelihood 10 September 2020, 15:35 UTC
61b2e1c Copyright 10 September 2020, 13:26 UTC
6aee724 More tests 10 September 2020, 12:42 UTC
0c699fc Add student t test 10 September 2020, 09:56 UTC
d43a17f Fix notebook 10 September 2020, 09:26 UTC
3a5aceb Remove multioutput from PR 10 September 2020, 09:20 UTC
6c36435 Fix test 10 September 2020, 09:16 UTC
6280674 Work 09 September 2020, 17:12 UTC
4af82f2 Merge branch 'gustavocmv/quadrature-likelihood' of github.com:GPflow/GPflow into vincent/st/heteroscedastic 08 September 2020, 15:59 UTC
077f7c9 removed print and tf.print 02 September 2020, 17:57 UTC
51ba7d9 removed print and tf.print 02 September 2020, 17:56 UTC
ced9428 removed unecessary tf.init_scope 02 September 2020, 17:56 UTC
b6f1bbc Merge branch 'gustavocmv/quadrature-likelihood' of https://github.com/GPflow/GPflow into gustavocmv/quadrature-likelihood 02 September 2020, 17:23 UTC
de00187 Merge branch 'develop' into gustavocmv/quadrature-likelihood 02 September 2020, 12:59 UTC
5a945d6 Broadcasting constant and zero mean function (#1550) * Broadcasting constant and zero mean function * Use rank instead of ndim 27 August 2020, 11:07 UTC
903b60d Update min TFP supported version to 0.10 (#1551) 27 August 2020, 10:50 UTC
aedb5a0 Merge branch 'develop' into gustavocmv/quadrature-likelihood 24 August 2020, 18:59 UTC
d025f96 Change shape of quadrature tensors for better broadcasting (#1542) * using the first dimension to hold the quadrature summation * adapting ndiagquad wrapper * Changed bf for bX in docstrings Co-authored-by: Gustavo Carvalho <gustavo.carvalho@delfosim.com> Co-authored-by: st-- <st--@users.noreply.github.com> Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> 24 August 2020, 18:54 UTC
6894af5 Fix for quadrature failure mode when autograph was set to False (#1548) * Fix and test 24 August 2020, 10:55 UTC
8c65ef6 Update parameter to be savable (#1518) 17 August 2020, 13:26 UTC
4682722 Update to not use custom image (#1545) * Update to not use custom image * Add test requirements 14 August 2020, 09:53 UTC
79b1a0b check dependency versions are valid on CI (#1536) 13 August 2020, 12:09 UTC
f9eb123 Re-introduce pytest-xdist (#1541) Enables pytest-xdist for locally running tests (`make test`) on multiple cores in parallel. 13 August 2020, 11:46 UTC
6bb7df9 Bump version numbers to 2.1.0. (#1544) 13 August 2020, 10:08 UTC
ca28e95 merged with gustavocmv/quadrature-change-shape 05 August 2020, 00:30 UTC
5744b51 Fixed separate_independent_conditional to correctly handle q_sqrt=None. (#1533) * Fixed separate_independent_conditional to correctly handle q_sqrt=None. Co-authored-by: Aidan Scannell <scannell.aidan@gmail.com> Co-authored-by: st-- <st--@users.noreply.github.com> 04 August 2020, 17:31 UTC
fa63a66 Merge branch 'gustavocmv/quadrature-change-shape' into gustavocmv/quadrature-likelihood 04 August 2020, 11:48 UTC
20c5ee4 Add base_conditional_with_lm function (#1528) * Added base_conditional_with_lm function, which accepts Lm instead of Kmm Co-authored-by: Neil Ferguson <neil@prowler.io> Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> Co-authored-by: st-- <st--@users.noreply.github.com> 03 August 2020, 14:38 UTC
be0e6e8 adapting ndiagquad wrapper 03 August 2020, 00:19 UTC
03889e6 using the first dimension to hold the quadrature summation 02 August 2020, 14:12 UTC
374139f fix 01 August 2020, 22:07 UTC
0d71e30 added QuadratureLikelihood to base, refactored ScalarLikelihood to use it 01 August 2020, 21:55 UTC
b3a2210 testing 01 August 2020, 19:29 UTC
d995194 Quadrature Refactoring (#1505) * WIP: quadrature refactoring * Removing old ndiagquad code * deleted test code * formatting and type-hint * merge modules * black formatting * formatting * solving failing tests * fixing failing tests * fixes * adapting tests for new syntax, keeping numerical behavior * black formatting * remove printf * changed code for compiled tf compatibility * black * restored to original version * undoing changes * renaming * renaming * renaming * reshape kwargs * quadrature along axis=-2, simplified broadcasting * black * docs * docs * helper function * docstrings and typing * added new and old quadrature equivalence tests * black * Removing comments Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> * Typo Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> * notation Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> * reshape_Z_dZ return docstring fix * FIX: quad_old computed with the ndiagquad_old Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> * more readable implementation Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> * tf.ensure_shape added * removed ndiagquad * removed ndiagquad * Revert "removed ndiagquad" This reverts commit 7bb0e9f1e0f2b0e225a2b8a5b3092c4c2f24ba91. * FIX: shape checking of dZ * Revert "removed ndiagquad" This reverts commit 8e235241a697696e361158c30ff9aa9b4cc69f8a. Co-authored-by: Gustavo Carvalho <gustavo.carvalho@delfosim.com> Co-authored-by: ST John <st@prowler.io> Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> 30 July 2020, 11:58 UTC
65aea21 pin tensorflow<2.3 tensorflow-probability<0.11 (#1537) 30 July 2020, 10:13 UTC
3c17a7d Fix formatting in docs (intro.md) and restore link removed by #1498 (#1520) 17 July 2020, 13:13 UTC
937222e fix bug in varying_noise notebook (#1526) 16 July 2020, 20:02 UTC
f1842a9 Update readme with new project using GPflow (#1530) 16 July 2020, 10:25 UTC
d69b17d Temporary workaround for tensorflow_probability dependency issue (#1522) * pin cloudpickle==1.3.0 as temporary workaround for tensorflow/probability#991 to unblock our build (to be reverted once fixed upstream) 06 July 2020, 10:31 UTC
34b023a Merge pull request #1512 from GPflow/master Update develop with master 02 July 2020, 15:32 UTC
965189d Update pull request template (#1510) Clarify template to make it easier for contributors to fill in relevant information. 02 July 2020, 10:10 UTC
acaccfd updated models.gpr docstring (#1511) Doc update. Resolves https://github.com/GPflow/docs/issues/4 * updated models.gpr docstring * Elaboration. Co-authored-by: Pola Elisabeth Schwobel <posc@MacBook-Pro.local> Co-authored-by: Mark van der Wilk <markvanderw@gmail.com> 23 June 2020, 10:52 UTC
5a63f66 Merge branch 'develop' into st/heteroskedastic 18 June 2020, 08:39 UTC
23769a1 Adding heteroskedastic tests (#1508) These tests ensure that heteroskedastic likelihood with a constant variance, will give the same results as a Gaussian likelihood with the same variance. 18 June 2020, 08:37 UTC
31dbbe5 Merge pull request #1506 from GPflow/develop Release 2.0.5 11 June 2020, 14:37 UTC
3669d13 bump version to 2.0.5 (#1504) 11 June 2020, 13:18 UTC
7db2276 fix type in Parameter type check (#1500) 11 June 2020, 10:59 UTC
a9e125e Ensure the plots appear in the generated documentation. (#1503) 11 June 2020, 09:05 UTC
390e4f0 Update link to distill article on GPs (#1498) Note that this links to a *different* article from the previous one - we will add the old link back in as well once it is back online. 10 June 2020, 12:55 UTC
e0a78b6 add comment 08 June 2020, 16:17 UTC
db4a9b1 note and bugfix 08 June 2020, 16:15 UTC
77eacca Supporting preslicing of multi-output combination kernels (#1495) 04 June 2020, 16:03 UTC
6fda0e9 improve NaturalGradient optimizer documentation and add shape checks (#1489) As discussed in #878, GPflow's NaturalGradient optimizer does not implement the diagonal covariance parametrization (`q_diag=True`). This PR clarifies this in the documentation and adds extra shape checks. 04 June 2020, 14:24 UTC
647ca90 Corrected variables name in convolutional notebook for better understanding (#1492) 02 June 2020, 15:09 UTC
12243a6 clean up Scipy types & code (#1454) Doc improvement: Fixes some typos in the Scipy docstring and adds a note on scipy minimize()'s callback argument vs GPflow Scipy().minimize()'s step_callback. Cleans up types in the module. Backwards-incompatible change: the `step_callback` that can be passes to the Scipy.minimize() method is changed to take its arguments by position, not name; in line with the StepCallback type signature (and in line with Python's typing.Callable documentation which suggests that callbacks should take arguments preferentially by position, not name). 02 June 2020, 12:16 UTC
89af61e quickfix to enable GPR to be used with variable data (#1490) GPR used the X.shape attribute instead of calling tf.shape(X); this prevented using it with Variable data, which is now successfully demonstrated in a test. 01 June 2020, 16:12 UTC
d0c78d0 Allow users to pass an iterable to set_trainable (#1486) 28 May 2020, 16:04 UTC
3ed381c Improve contributing.md (#1488) * bring contributing.md up to date (resolves #1474) Co-authored-by: joelberkeley-pio <joel.berkeley@prowler.io> 28 May 2020, 12:25 UTC
d4d8a99 Merge branch 'develop' into st/heteroskedastic 28 May 2020, 09:22 UTC
d12be33 add type hints: inducing_variables (#1487) 27 May 2020, 19:30 UTC
1929a36 Makefile quickfix (#1482) Fixes a syntax error in the Makefile introduced by #1471. Also adds a `format-check` target for black --check and a `check-all` target that runs format-check, type-check and the pytest tests. 27 May 2020, 16:39 UTC
4dd0447 Merge branch 'develop' of github.com:GPflow/GPflow into st/heteroskedastic 26 May 2020, 10:56 UTC
435a7ff Merge pull request #1481 from GPflow/develop Release 2.0.4 20 May 2020, 13:59 UTC
f8676eb bump version to 2.0.4 (#1478) 20 May 2020, 12:19 UTC
a198764 enable mypy on CI (#1471) 19 May 2020, 13:50 UTC
fc13c08 Merge branch 'develop' into st/heteroskedastic 19 May 2020, 10:12 UTC
61f8d84 Fix freeze and traverse utility methods (#1476) TensorFlow Probability 0.10 introduced a new _parameters attribute in tfp.bijectors.Bijector instances that contains a self-reference, which broke GPflow's module-traversion utilities (leaf_components, print_summary, deepcopy, freeze). This PR changes traverse_module to ignore the _parameters attribute and proposes a new deepcopy approach that simply uses copy.deepcopy()'s memo argument. Co-authored-by: st-- <st--@users.noreply.github.com> 18 May 2020, 20:58 UTC
150a0d1 add type hints to gpflow.base (#1427) 14 May 2020, 13:37 UTC
bf35d66 Merge pull request #1468 from GPflow/vincent/master_203 Sync develop with master 2.0.3 13 May 2020, 09:28 UTC
56c2efe Merge remote-tracking branch 'origin/develop' into vincent/master_203 13 May 2020, 09:05 UTC
a4bfbe6 Add ipynb to gitignore (#1466) * Add ipynb to gitignore 13 May 2020, 07:58 UTC
b83f124 Merge branch 'develop' 13 May 2020, 07:49 UTC
49ffbcf Merge branch 'master' into develop 13 May 2020, 07:48 UTC
00d2e66 bump version to 2.0.3 (#1464) 12 May 2020, 17:21 UTC
10a0c9d Notebook exemplifying HeteroskedasticTFPDistribution usage (#1462) * fixes * typo fix; reshaping fix * notebook showing how to use HeteroskedasticTFPDistribution likelihood * converting to .pct.py format * removed .ipynb * better descriptions * black auto-formatting Co-authored-by: Gustavo Carvalho <gustavo.carvalho@delfosim.com> 12 May 2020, 12:53 UTC
7560936 Update setup.py for tensorflow 2(.2) (#1460) 12 May 2020, 12:44 UTC
310786b Merge remote-tracking branch 'origin' into st/heteroskedastic 11 May 2020, 14:27 UTC
5e599fb Release 2.0.2 (#1459) * add long_description and project_urls to setup.py (#1438) * add type hints for probability distributions (#1421) * remove comment (#1441) * Use a type alias in the fnction signature of leading_transpose (#1442) * refactor natgrads to be more efficient (#1443) * Fix dimensions of kernel evaluation of changepoint kernel (#1446) * Removed unusued imports. (#1450) * Improve representation of GPflow objects in IPython/Jupyter notebook (#1453) * includes the repr() string in IPython/Jupyter notebook representation as well (i.e. fully-qualified class name and object hash (memory address), which helps distinguish objects from each other) * only displays the parameter table when it is not empty * makes use of default_summary_fmt() for IPython shell * Convert data structures to tensor in model init method (#1452) * Use a boolean for full covariance in sample_mvn. (#1448) * #1452 for GPMC model (#1458) * release candidate v2.0.2 (#1457) Co-authored-by: st-- <st--@users.noreply.github.com> Co-authored-by: joelberkeley-pio <joel.berkeley@prowler.io> Co-authored-by: John Mcleod <43960404+johnamcleod@users.noreply.github.com> Co-authored-by: Mark van der Wilk <markvanderw@gmail.com> Co-authored-by: Artem Artemev <art.art.v@gmail.com> 07 May 2020, 15:01 UTC
6ce4203 release candidate v2.0.2 (#1457) 07 May 2020, 14:45 UTC
8f06b7c #1452 for GPMC model (#1458) 07 May 2020, 14:24 UTC
39d563c Use a boolean for full covariance in sample_mvn. (#1448) 07 May 2020, 13:00 UTC
7e3e514 Convert data structures to tensor in model init method (#1452) Resolves #1439 07 May 2020, 12:22 UTC
bcd9613 multioutput likelihood WIP 04 May 2020, 23:00 UTC
daadda4 cleanup heteroskedastic 04 May 2020, 22:59 UTC
5dc0f48 cleanup 04 May 2020, 22:54 UTC
e07985a Merge remote-tracking branch 'origin' into st/heteroskedastic 04 May 2020, 16:39 UTC
5ec7e91 Improve representation of GPflow objects in IPython/Jupyter notebook (#1453) * includes the repr() string in IPython/Jupyter notebook representation as well (i.e. fully-qualified class name and object hash (memory address), which helps distinguish objects from each other) * only displays the parameter table when it is not empty * makes use of default_summary_fmt() for IPython shell 04 May 2020, 13:13 UTC
08739ce Removed unusued imports. (#1450) 02 May 2020, 18:11 UTC
8b24183 Fix dimensions of kernel evaluation of changepoint kernel (#1446) Closes #1440 26 April 2020, 21:36 UTC
b41d4f3 refactor natgrads to be more efficient (#1443) Previously, GPflow's NaturalGradient optimizer would call the loss_function once for each (q_mu, q_sqrt) set in the var_list. This is a light refactor that separates out applying the natural gradient step from computing the gradients (`_natgrad_apply_gradients`), and changes `_natgrad_steps` to only evaluate the loss function once, computing the gradients for all (q_mu, q_sqrt) tuples passed in the var_list. Other changes: - The no-longer-used `_natgrad_step` method got removed. - NaturalGradient now takes a `xi_transform` argument that is used for all parameter sets without explicitly specified xi transform (i.e. tuples rather than triplets). - XiTransform has been changed to have staticmethods. None of this should affect any downstream code; this PR is backwards-compatible. 23 April 2020, 18:17 UTC
c7550ce Use a type alias in the function signature of leading_transpose (#1442) Ensure that the `leading_transpose` function can be used with the @tf.function decorator (workaround for bug in tensorflow<=2.2.0rc3) 23 April 2020, 09:19 UTC
82f2db4 remove comment (#1441) 20 April 2020, 22:03 UTC
e1a3fa3 add type hints for probability distributions (#1421) 20 April 2020, 09:38 UTC
ca3b854 add long_description and project_urls to setup.py (#1438) 20 April 2020, 07:43 UTC
2358539 Release 2.0.1 (#1436) Release notes: - Improve structure of likelihoods subdirectory (#1416) - Update README.md (#1401) and GPflow 2 upgrade guide (#1414) - Improved handling of invalid values for constrained Parameters (#1408) - Improvements on types/function annotations (#1406, #1420) - Documentation improvements (metalearning with GPs: #1382, coregionalization notebook: #1402, MCMC notebook: #1410, intro to gpflow with tensorflow 2: #1413) - Minor documentation fixes (#1429, #1430, #1433) - Fix: move matplotlib import inside ImageToTensorBoard (#1399) - Fix: tf.function compilation of ndiagquad (#1418) - Fix: cache tensorboard file writers and re-use them (#1424) 15 April 2020, 12:19 UTC
3fc050d Merge master (at 2.0.0) into develop (pull request #1437) 15 April 2020, 11:33 UTC
641b8ad Merge branch 'develop' of github.com:GPflow/GPflow into develop-master-merge 15 April 2020, 10:48 UTC
8afd2f9 Merge remote-tracking branch 'origin/master' into develop-master-merge 15 April 2020, 10:37 UTC
a6156e8 bump version to 2.0.1 (#1426) 15 April 2020, 10:14 UTC
2018243 fix kernel construction in multioutput notebook (#1430) * fix kernel construction in multioutput notebook * fix one more kernel in changepoints notebook 15 April 2020, 10:14 UTC
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