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df64611 black 15 September 2020, 15:23 UTC
414dc29 DONE: swap n_gh for num_gauss_hermite_points 15 September 2020, 15:16 UTC
e8daecd Merge branch 'gustavocmv/quadrature-likelihood' into vincent/st/heteroscedastic 15 September 2020, 14:54 UTC
9bf71d4 Merge branch 'develop' into gustavocmv/quadrature-likelihood 15 September 2020, 12:42 UTC
799b659 Scalar Likelihood Refactoring (#1566) * refactoring scalar likelihood * adding dtype casts to quadrature * black Co-authored-by: Gustavo Carvalho <gustavo.carvalho@delfosim.com> Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> 15 September 2020, 12:36 UTC
e6f9ac7 small merging fixes 14 September 2020, 18:01 UTC
3a7915d Merge branch 'gustavocmv/scalar-likelihood-refactor' into gustavocmv/quadrature-likelihood 14 September 2020, 17:58 UTC
0336b27 Merge pull request #1564 from GPflow/st/remerge_master_210 Merge master back into develop 14 September 2020, 17:00 UTC
d51c487 Merge branch 'develop' into st/remerge_master_210 14 September 2020, 16:39 UTC
234a734 Merge remote-tracking branch 'origin/master' into st/remerge_master_210 14 September 2020, 16:38 UTC
5c49580 bump version to 2.1.1 (#1562) 14 September 2020, 16:33 UTC
5baf4ee black 11 September 2020, 16:03 UTC
59517d7 adding dtype casts to quadrature 11 September 2020, 16:02 UTC
ae8b2e5 refactoring scalar likelihood 11 September 2020, 16:02 UTC
c852ccf black 10 September 2020, 14:34 UTC
85844cc fixed bad commenting 10 September 2020, 14:31 UTC
cd12da8 removing NDiagGHQuadratureLikelihood from test 10 September 2020, 14:28 UTC
9bb80ff bugfix 10 September 2020, 14:26 UTC
a24b224 black 10 September 2020, 14:17 UTC
274c8dd Merge branch 'gustavocmv/quadrature-likelihood' of https://github.com/GPflow/GPflow into gustavocmv/quadrature-likelihood 10 September 2020, 14:15 UTC
108755a removed NDiagGHQuadratureLikelihood from test 10 September 2020, 14:11 UTC
2a32d8c n_gh ---> num_gauss_hermite_points 10 September 2020, 14:11 UTC
5db53ca Merge branch 'develop' into gustavocmv/quadrature-likelihood 10 September 2020, 14:08 UTC
e4a0dcf _set_latent_and_observation_dimension_eagerly 10 September 2020, 13:42 UTC
67e583c Fix SGPR upper bound for non zero mean functions (#1560) 10 September 2020, 13:41 UTC
44fb6f2 Removed NDiagGHQuadratureLikelihood class in favor of non-abstract QuadratureLikelihood 10 September 2020, 13:34 UTC
61b2e1c Copyright 10 September 2020, 13:26 UTC
d15d8c5 Merge branch 'gustavocmv/quadrature-likelihood' of https://github.com/GPflow/GPflow into gustavocmv/quadrature-likelihood 10 September 2020, 13:15 UTC
6aee724 More tests 10 September 2020, 12:42 UTC
a0df00c add license text to all gpflow submodules (#1480) Adds Copyright notice and Apache license text (short form) to the preamble of all python files underneath gpflow/. Also unifies the copyright notice to simply state "The GPflow Contributors" to simplify maintenance of the copyright notices (this does not affect who holds copyright). 10 September 2020, 11:45 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
650d17e Type annotations Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> 08 September 2020, 17:57 UTC
4af82f2 Merge branch 'gustavocmv/quadrature-likelihood' of github.com:GPflow/GPflow into vincent/st/heteroscedastic 08 September 2020, 15:59 UTC
7b2a0c8 Fixes for tf 2.3 / tfp 0.11.0 compatiblity (#1553) * tensorflow_probability has been changing internals around their caching; here we update the cache-clearing for our deepcopy so that it works both for tensorflow_probability < 0.11.0, == 0.11.0 (with a workaround for the bug contained therein), and > 0.11.0 (in their master branch they fixed the bug and changed internals again) * revert pinning of tf/tfp, numpy, scipy; rely on `pip --use-feature=2020-resolver` * pin black==19.10b0 as the 20.8b0 upgrade changes formatting a lot * disable test broken by tensorflow 2.3 Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> 08 September 2020, 15:44 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
f3c5110 Release 2.1.0 (#1552) * Update pull request template (#1510) Clarify template to make it easier for contributors to fill in relevant information. * 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) * Update readme with new project using GPflow (#1530) * fix bug in varying_noise notebook (#1526) * Fix formatting in docs (intro.md) and restore link removed by #1498 (#1520) * pin tensorflow<2.3 tensorflow-probability<0.11 (#1537) * 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> * 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> * 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> * Bump version numbers to 2.1.0. (#1544) * Re-introduce pytest-xdist (#1541) Enables pytest-xdist for locally running tests (`make test`) on multiple cores in parallel. * check dependency versions are valid on CI (#1536) * Update to not use custom image (#1545) * Update to not use custom image * Add test requirements * Update parameter to be savable (#1518) * Fix for quadrature failure mode when autograph was set to False (#1548) * Fix and test * 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> * Update min TFP supported version to 0.10 (#1551) * Broadcasting constant and zero mean function (#1550) * Broadcasting constant and zero mean function * Use rank instead of ndim Co-authored-by: st-- <st--@users.noreply.github.com> Co-authored-by: joelberkeley-pio <joel.berkeley@prowler.io> Co-authored-by: gustavocmv <47801305+gustavocmv@users.noreply.github.com> Co-authored-by: Gustavo Carvalho <gustavo.carvalho@delfosim.com> Co-authored-by: ST John <st@prowler.io> Co-authored-by: Neil Ferguson <nfergu@users.noreply.github.com> Co-authored-by: Neil Ferguson <neil@prowler.io> Co-authored-by: Aidan Scannell <as12528@my.bristol.ac.uk> Co-authored-by: Aidan Scannell <scannell.aidan@gmail.com> Co-authored-by: Sandeep Tailor <s.tailor@insysion.net> Co-authored-by: Artem Artemev <art.art.v@gmail.com> 27 August 2020, 11:22 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
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