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a228884 Merge branch 'develop' into st/quickfix_num_latent 17 July 2020, 13:13 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
3845895 Merge branch 'develop' into st/quickfix_num_latent 16 July 2020, 10:27 UTC
f1842a9 Update readme with new project using GPflow (#1530) 16 July 2020, 10:25 UTC
fdeb993 Merge branch 'develop' into st/quickfix_num_latent 06 July 2020, 11:13 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
2b7bc4f Merge branch 'develop' into st/quickfix_num_latent 02 July 2020, 10:31 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
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
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
bdbd2c4 Merge branch 'develop' into st/quickfix_num_latent 01 June 2020, 11:24 UTC
d0c78d0 Allow users to pass an iterable to set_trainable (#1486) 28 May 2020, 16:04 UTC
8cbcbde Merge branch 'develop' into st/quickfix_num_latent 28 May 2020, 13:41 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
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
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
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
f46cf97 turn into keyword arg 14 May 2020, 15:15 UTC
3c45748 Merge remote-tracking branch 'origin/develop' into st/quickfix_num_latent 14 May 2020, 15:12 UTC
150a0d1 add type hints to gpflow.base (#1427) 14 May 2020, 13:37 UTC
a635212 Merge branch 'develop' into st/quickfix_num_latent 14 May 2020, 13:10 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
7560936 Update setup.py for tensorflow 2(.2) (#1460) 12 May 2020, 12:44 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
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
3fd78aa fix other-issue.md issue template (#1432) The "other issue" template wasn't being pulled in by GitHub's "new issue chooser"(https://github.com/GPflow/GPflow/issues/new/choose) because of a parsing failure due to the use of quotes in the name: field, which is fixed by this PR (changed version obtained by putting the text with quotes into GitHub's "create an issue template" interface). Includes a few minor copyedits. 14 April 2020, 16:57 UTC
5a5603d fix pyplot import in notebooks (#1433) * fix pyplot import for matplotlib 3.1.3 (closes #1423) * apply same fix to other notebooks 14 April 2020, 16:56 UTC
4821d03 Issue templates (#1425) This gives the GPflow repository four issue templates: * bugs (including performance and build issues) * feature requests * documentation issues * other issues (pointing to the stackoverflow gpflow tag) This will hopefully make new issues more easily addressable. :) Co-authored-by: joelberkeley-pio <joel.berkeley@prowler.io> 14 April 2020, 14:59 UTC
806004d fix link in sphinx intro.rst (#1429) Closes #1428. 14 April 2020, 12:57 UTC
12dafe9 move matplotlib import inside ImageToTensorBoard (#1399) * move matplotlib import inside ImageToTensorBoard class so that it is not a hard dependency for GPflow (`import gpflow` does not require matplotlib, only instantiating `ImageToTensorBoard` does) * split up monitor into base.py and tensorboard.py * add matplotlib to extras_require 14 April 2020, 09:55 UTC
e652e75 Fix issue where multiple file writers were created (#1424) Cache summary file writers and re-use them in ToTensorBoard monitor task. Fixes #1385 10 April 2020, 20:28 UTC
8e8ea85 type ci utils module (#1420) 09 April 2020, 21:07 UTC
6388133 Improve user experience on invalid assignments to constrained Parameters (#1408) Addresses #1407. * attempt to improve the error message in the gpflow.Parameter check on assigning a new value that is incompatible with the parameter's transform (e.g. a non-positive value to a parameter with a positive() transform) * Gaussian likelihood: add explicit `__init__`-time check that variance > variance_lower_bound, add `__init__` docstring, move "default variance lower bound" magic number into class-level constant * change gpflow.config's positive_minimum to always be a float (initialized to 0.0 by default) 08 April 2020, 13:52 UTC
92f914d fix compilation issue in ndiagquad when integrating over multiple dimensions (#1418) 08 April 2020, 13:45 UTC
5c89c1e Improve structure of likelihoods subdirectory (#1416) Addresses #1405 * New structure underneath gpflow/likelihoods/: * base.py: all base classes (Likelihood, MonteCarloLikelihood, ScalarLikelihood) and SwitchedLikelihood * multiclass.py: multi-class classification (Softmax, MultiClass + RobustMax) * scalar_continuous.py: continuous-Y subclasses of ScalarLikelihood (Gaussian, StudentT, Exponential, Beta, Gamma) * scalar_discrete.py: discrete-Y subclasses of ScalarLikelihood (Bernoulli, Poisson, Ordinal) * utils.py: the `inv_probit` link function used by Bernoulli and Beta likelihoods * misc.py: GaussianMC - used for demonstration/tests only. (Note that usage, i.e. accessing gpflow.likelihoods.<LikelihoodClass>, has not changed.) * Tests for multi-class classification likelihoods moved out into their own test module (including stubs for the missing MultiClass quadrature tests of #1091) * Re-activates the quadrature tests for ScalarLikelihood subclasses with analytic variational_expectations/predict_log_density/predict_mean_and_var that inadvertently got disabled by #1334 * Fixes a bug in Bernoulli._predict_log_density that was uncovered by these tests * Fixes random seed for mock data generation in test_natural_gradient to make svgp_vs_gpr test pass again 08 April 2020, 09:48 UTC
dda8c39 update gpflow2 upgrade guide: likelihood section, predict_log_density, IsotropicStationary (#1414) 08 April 2020, 09:25 UTC
e7cfb8e Match original experimental setup for "metalearning with GPs" notebook. (#1382) * Match original experiment setup from paper. Replicate the original setup published in Fortuin and Ratsch (2019) and heavily comment the code with references to the paper. * Run `make format` and reduce hyperparameters to ease computation. * Format MSE and std to 2 decimals and sort randomly permuted indices. * Describe experimental modifications made in the notebook. * Plot target task training points. * Plot prediction variance/uncertainty. * Go with N=500, use more explicit name. * Address comments from @st-- 07 April 2020, 19:38 UTC
8094187 Use AUTOTUNE from tf.data.experimental (#1413) Best practice demonstrated in our notebooks 06 April 2020, 11:56 UTC
90f9a12 Fix MCMC sampler in documentation (#1410) * Increase MCMC sampling * Fix section links 03 April 2020, 17:04 UTC
ea10dea Fix mypy errors -variables are not types- (#1406) 03 April 2020, 13:12 UTC
7417180 update README for 2.0 release (#1401) 02 April 2020, 11:49 UTC
4dddadc Add clarity to coregionalization example (#1402) 01 April 2020, 13:40 UTC
1b023cb fixup website (#1398) 31 March 2020, 18:50 UTC
59f3e2c Update circleci to TF2.1 docker image (#1397) 31 March 2020, 15:15 UTC
47e788a Release 2.0.0 (#1396) 31 March 2020, 13:19 UTC
4f9aff7 Bump version to 2.0.0 (#1395) 31 March 2020, 13:04 UTC
7e717cc refactor training objective methods (#1276) This gives all `BayesianModel` subclasses a consistent interface both for optimization (MLE/MAP) and MCMC. Models are required to implement `maximum_log_likelihood_objective`, which is to be maximized for model training. Optimization: The `_training_loss` method is defined as `- (maximum_log_likelihood_objective + log_prior_density)`. This is exposed by the InternalDataTrainingLossMixin and ExternalDataTrainingLossMixin classes. For models that keep hold of the data internally, `training_loss` can directly be passed as a closure to an optimizer's `minimize`, for example: ```python model = gpflow.models.GPR(data, ...) gpflow.optimizers.Scipy().minimize(model.training_loss, model.trainable_variables) ``` If the model objective requires data to be passed in, a closure can be constructed on the fly using `model.training_loss_closure(data)`, which returns a no-argument closure: ```python model = gpflow.models.SVGP(...) gpflow.optimizers.Scipy().minimize( model.training_loss_closure(data), model.trainable_variables, ... ) ``` The training_loss_closure() method provided by both InternalDataTrainingLossMixin and ExternalDataTrainingLossMixin takes a boolean `compile` argument (default: True) that wraps the returned closure in tf.function(). Note that the return value should be cached in a variable if the minimize() step is run several times to avoid re-compilation in each step! MCMC: The `log_posterior_density` method can be directly passed to the `SamplingHelper`. By default, `log_posterior_density` is implemented as `maximum_log_likelihood_objective + log_prior_density`. Models can override this if needed. Example: ```python model = gpflow.models.GPMC(...) hmc_helper = gpflow.optimizers.SamplingHelper( model.log_posterior_density, model.trainable_parameters ) hmc = tfp.mcmc.HamiltonianMonteCarlo( target_log_prob_fn=hmc_helper.target_log_prob_fn, ... ) ``` In this case, the function that runs the MCMC chain should be wrapped in tf.function() (see MCMC notebook). 31 March 2020, 12:17 UTC
e61ee69 Add a section about custom user config (#1394) 31 March 2020, 10:00 UTC
27bc0d4 _scalar_log_density -> _scalar_log_prob (#1393) In GPflow2, the log probability density itself (summed over multiple outputs, if applicable) was called log_prob to be consistent with tensorflow_probability. In #1334 the element-wise log probability density to be implemented by ScalarLikelihood subclasses was called _scalar_log_density. This PR renames the latter to _scalar_log_prob to make it more self-consistent. 31 March 2020, 08:39 UTC
baa8bee Update upgrade guide (#1390) 31 March 2020, 08:29 UTC
d2ac01f Improve doc generation (#1391) * clarifying doc generation * add automodule for module level docstrings 31 March 2020, 08:23 UTC
72de787 rename jit to compile (#1392) 30 March 2020, 17:58 UTC
1e936e0 Increased tolerance for sqrt in kernels K_r2. (#1388) We had a report of numerical problems when the tolerance was 1e-40. So in GPflow 1 it got changed to 1e-36, but this wasn't ported to GPflow 2, hence why we're fixing it now. 30 March 2020, 12:08 UTC
792201d Added suggestion on how to open TensorBoard so it updates. (#1389) 30 March 2020, 11:35 UTC
c8e8f00 enable pickling of frozen models (#1338) Changes setattr_by_path to delete the attribute before setting it again. When simply replacing a Parameter with tf.Constant, tensorflow did not update its internal list of tracked variables, which prevented deepcopying and pickling of frozen models. Explicitly deleting the tracked variable before assigning a constant value forces tensorflow to update its state. Workaround for https://github.com/tensorflow/tensorflow/issues/37806 30 March 2020, 11:20 UTC
0b9e1f0 MCMC cleanup (#1374) * SamplingHelper: clean up docstrings * SamplingHelper: do not convert to numpy in convert_to_constrained_samples * MCMC notebook: clean up; make faster (ci_niter); remove opaque use of utility function * MCMC notebook: clarify MCMC over Z for SGPMC - inducing points should be non-trainable * tests: use pytest.raises * tests: clean up match argument 30 March 2020, 11:17 UTC
1272141 fix notebook LaTeX equations + upgrade guide link (#1370) * fix notebook LaTeX equations * remove empty cells at bottom of notebooks * fix link to intro_to_gpflow2 in docs * Apply suggestions from code review Co-Authored-By: Vincent Dutordoir <dutordoirv@gmail.com> * fix internal notebook link * more fixes Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> 30 March 2020, 10:33 UTC
aff62bc Make Scipy more robust & faster (#1377) * Adds an explicit check to Scipy() that all elements of `variables` are actually tf.Variable instances (unconstrained variables) - accidentally passing `model.trainable_parameters` may work but give the wrong answers for parameters with transforms! Passing `model.trainable_variables` is the right thing to do. * Updates _compute_loss_and_gradients to only compute gradients wrt passed-in variables. * Fix mixture density network notebook, which had erroneously passed model.trainable_parameters instead of model.trainable_variables. 30 March 2020, 09:32 UTC
d41d6eb Set kernelspec to Py3 in monitoring.pct.py (#1386) Quickfix for the failing monitoring.pct.py notebook during the doc generation on CircleCi. Problem was caused by an unknown Python version in the notebook's kernelspec. It has to be 'name: python3', whereas conda may add a user-specific custom name there. 30 March 2020, 08:49 UTC
82999c9 minimum required multipledispatch version is 0.6 (#1384) As shown by #1381, gpflow does not work with older versions of multipledispatch - this change reflects this in the setup.py version requirements. 30 March 2020, 08:47 UTC
7ec7955 speed up VFF notebook (#1383) 28 March 2020, 16:12 UTC
30824d2 Cleaning some todo (#1347) 27 March 2020, 18:15 UTC
0d97bc0 MCMC notebook prior update & helper refactoring (#1372) 27 March 2020, 16:57 UTC
cf35758 moved multioutput module files (#1353) Moved all `mo_` files to be in their own multioutput directory. This should be more sustainable as the number of multioutput items increases 27 March 2020, 15:23 UTC
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