https://github.com/GPflow/GPflow

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bf8e2b9 fix script 15 September 2021, 16:31 UTC
d11994d Merge pull request #1710 from GPflow/fergus/hetgpr Start to simplify hetgpr 15 September 2021, 15:21 UTC
01a1eaf Simplify 15 September 2021, 15:20 UTC
e4bf1bf Start to simplify hetgpr 09 September 2021, 13:12 UTC
ca89ac6 Merge pull request #1707 from GPflow/john/linear Use HeteroskedasticTFP likelihood 23 August 2021, 11:38 UTC
bf3bd5f Use HeteroskedasticTFP likelihood 23 August 2021, 09:48 UTC
7917b42 Fix lml evaluation of het_gpr 29 July 2021, 16:48 UTC
a0a3439 Add script 29 July 2021, 14:47 UTC
91b640b Enabled predictions for hetGPR 29 July 2021, 14:40 UTC
7ea600b Add het likelihood 29 July 2021, 13:03 UTC
c923b3f Add het likelihood 29 July 2021, 13:03 UTC
888f886 Add draft of het gpr notebook 28 July 2021, 15:53 UTC
bef54f4 Add draft of het gpr notebook 28 July 2021, 15:53 UTC
487468e Introduced outline of heteroscedastic GPR model 27 July 2021, 16:07 UTC
3e4b9f1 Update RELEASE.md (#1701) Add PR references to release notes 06 July 2021, 08:24 UTC
6c9ed3a John/parameters (#1699) 02 July 2021, 14:51 UTC
f14c41e Andrewl cache gpr (#1696) 01 July 2021, 14:42 UTC
268e315 Small refactor of the posteriors to support other models (#1695) 22 June 2021, 14:59 UTC
bebbc2b fixes to remove erroneous deprecation warnings (#1693) * fix import to remove erroneous deprecation warning * also fix deprecation warnings for conditional * update RELEASE.md 18 June 2021, 13:45 UTC
4054c53 upgrade to black==20.8b1 (#1694) * upgrade to black==20.8b1 * update black version in CircleCI config as well * update RELEASE.md * add types-pkg_resources tests dependency * install types-pkg_resources in CircleCI too 18 June 2021, 07:15 UTC
55690c7 Fix unit test which fails when running with TensorFlow 2.5.0 (#1684) 17 May 2021, 12:39 UTC
b93548d Bugfix for new Posterior object with PrecomputeCacheType.VARIABLE (#1678) 29 April 2021, 11:29 UTC
1205617 bump version and update RELEASE.md (#1676) 27 April 2021, 17:13 UTC
b4e6298 Posterior object for fast predictions (#1636) GPflow had already been optimised for speed in the training loop. This PR addresses the speed of predictions and resolves (partially) #1599. We achieve this by introducing new Posterior objects that can cache the results of a "precompute" stage (everything that's independent of test points) and thereby significantly speeds up repeated predictions. Co-authored-by: ST John <st--@users.noreply.github.com> Co-authored-by: stefanos <stefanosele@users.no-reply.github.com> Co-authored-by: John Mcleod <43960404+johnamcleod@users.noreply.github.com> 27 April 2021, 16:17 UTC
a8ee4ae Update HOWTO_RELEASE.md. (#1670) 22 April 2021, 21:45 UTC
1e1de82 Change URL for GPflow logo in README.md to absolute, so that it will render correctly on PyPI (#1669) 15 April 2021, 19:51 UTC
9f50087 Bump version to 2.1.5 (#1666) * Bump version to 2.1.5 * add release notes section for 2.2.0. 15 April 2021, 15:40 UTC
1d96af4 fix gpflow.config module-level docstring (#1664) 13 April 2021, 16:01 UTC
bfb60c0 John/iic whiten (#1663) * Add test with whiten * Make format * Update RELEASE.md Co-authored-by: st-- <st--@users.noreply.github.com> 13 April 2021, 14:22 UTC
0812cd3 John/fc whiten (#1662) * Add test for white=False * Make format * Update RELEASE.md 13 April 2021, 13:46 UTC
ea39cba Add RELEASE.md (#1661) * Add RELEASE.md inspired by TensorFlow and include in PR template * add HOWTO_RELEASE.md 12 April 2021, 15:35 UTC
4e6f9ce Clean up utilities subpackage (#1650) Separates gpflow.utilities.utilities into gpflow.utilities.misc and gpflow.utilities.traversal. Though user code ought to access all functions directly through gpflow.utilities, not its submodules, a backwards-compatible redirect is provided. Also moves tests around to improve module structure. 08 April 2021, 12:46 UTC
afb7699 bring back full list of all contributors throughout time (#1660) * bring back full list of all contributors throughout time * updated PR template * links to github accounts 06 April 2021, 10:44 UTC
21e5317 Proposed fix for the fully_correlated_conditional_repeat issue (#1652) Fixes #1651 06 April 2021, 10:15 UTC
5b76536 Fix fallback inducing points with multioutput Kuf. (#1654) Fixes #1653 06 April 2021, 09:31 UTC
405eb97 Update README.md (#1603) * reorganization of structure * update maintainers * update project list, including link to signature covariances project * table of contents 19 March 2021, 14:04 UTC
629e7b2 fix bug (that masked test failure!) in test_method_equivalence (#1649) * fix bug (that masked test failure!) in test_method_equivalence and improve collection speed * optimize non-whitened SVGP model more strongly to get test_equivalence to pass * remove --use-feature=2020-resolver (will become an error in pip 21.0) 15 March 2021, 17:16 UTC
1831a5d Update README and require TensorFlow>=2.2 (#1647) Add explanation of TensorFlow/TFP dependencies (as brought up by https://github.com/GPflow/GPflow/issues/1623) 07 March 2021, 14:05 UTC
94fa390 New _add_noise_cov method for GPR model class to make it more easily extensible (#1645) 25 February 2021, 16:12 UTC
3ea8731 Compatibility between Monitor API and SciPy optimizer (#1642) Co-authored-by: st-- <st--@users.noreply.github.com> 18 February 2021, 16:29 UTC
406d2d0 fix ModelToTensorBoard max_size = -1 (#1619) 03 February 2021, 13:45 UTC
797fed1 Mypy build fix (#1637) 03 February 2021, 12:38 UTC
bc04306 Quickfix dynamic shapes in quadrature (#1626) 13 January 2021, 16:31 UTC
721756a list structured-dgp as downstream project (#1621) Co-authored-by: st-- <st--@users.noreply.github.com> 12 January 2021, 12:31 UTC
7688477 Fix tests for TF 2.4/TFP 0.12 (#1625) * fix test_deepcopy * increase test_scipy_jit tolerance to make it pass 12 January 2021, 11:59 UTC
60e19f8 bump version to 2.1.4 (#1612) 01 December 2020, 11:59 UTC
61fc327 list trieste as downstream project (#1611) * list trieste as downstream project Co-authored-by: Joel Berkeley <joel.berkeley@secondmind.ai> Co-authored-by: st-- <st--@users.noreply.github.com> 26 November 2020, 17:14 UTC
282d1cd HeteroskedasticTFPConditional should construct tensors at class-construction, not at module-import time (#1598) 15 October 2020, 17:54 UTC
8562503 Replace len(inducing_variable) with inducing_variable.num inducing property (#1594) Adds support for inducing variables with dynamically changing shape. Change usage from `len(inducing_variable)` to `inducing_variable.num_inducing` instead. Resolves #1578. 08 October 2020, 15:04 UTC
9f95d87 bump version to 2.1.3 (#1590) 07 October 2020, 12:01 UTC
cfd1830 Doc requirements update (#1592) * update doc requirements * update copyright 07 October 2020, 11:46 UTC
638c4ed Bugfix for independent_interdomain_conditional (#1583) Resolves #818 Co-authored-by: ST John <st@secondmind.ai> 07 October 2020, 10:07 UTC
39c8a76 enable trigger-docs-generation for master branch as well (#1580) Co-authored-by: ST John <st@secondmind.ai> 06 October 2020, 15:25 UTC
3baf368 Remove tiling workaround for lack of broadcasting in previous TensorFlow versions (#1585) We used to tile in gauss_kl() to work around TensorFlow's lack of broadcasting. Since TensorFlow 2.2, this is finally working, and this PR removes the tiling for TensorFlow>=2.2. Resolves #1321. Co-authored-by: ST John <st@secondmind.ai> 06 October 2020, 15:03 UTC
e248051 update intro_to_gpflow2 notebook to account for saved_model now working (#1586) Co-authored-by: ST John <st@secondmind.ai> Co-authored-by: Sandeep Tailor <s.tailor@insysion.net> 06 October 2020, 14:12 UTC
98f7997 fix broken API docs (#1587) * move Version check inside reset_cache_bijectors to not confuse Sphinx * revert non-working "projects: 7" line in bugs issue template * fix code-block type in intro.rst 06 October 2020, 13:30 UTC
8dc912e Fix notebook heading levels and add links (#1579) * fix heading levels * add cross-references 06 October 2020, 12:37 UTC
7d6a6da Update issue templates (#1581) * automatically add bugs to bug project board * disable blank issues Co-authored-by: ST John <st@secondmind.ai> 05 October 2020, 15:50 UTC
b74e19e Explicit NotImplementedError on predict_y/predict_log_density with full_(output_)cov=True (#1582) Closes #1569 Co-authored-by: ST John <st@secondmind.ai> 05 October 2020, 10:48 UTC
8e0744a bump version to 2.1.2 (#1575) 30 September 2020, 16:57 UTC
65a79e4 isort for consistent imports (#1572) * GPflow now includes an isort check in its CI build. Run with `make format` / `make format-check`. 30 September 2020, 16:42 UTC
d618fe5 Likelihood quadrature cleanup (#1571) * Global constant for num_gauss_hermite_points default * QuadratureLikelihood with dependency injection (in preparation for unifying with MonteCarloLikelihood) * ScalarLikelihood as QuadratureLikelihood subclass (with _quadrature_dim/_quadrature_log_prob/_quadrature_reduction) * HeteroskedasticTFPConditional: rename argument to `scale_transform` and remove undocumented scaling * DeprecationWarning for deprecated code 30 September 2020, 13:54 UTC
12395be fix BijectorCache workaround (#1574) Follow-up to #1553 29 September 2020, 15:17 UTC
0d3684b add packaging to dependencies; add 'import gpflow' check (#1568) 17 September 2020, 15:33 UTC
ad6e031 Multi Latent Likelihoods using new quadrature Likelihoods (#1559) * HeteroskedasticLikelihood base class draft * fixup * cleanup * cleanup heteroskedastic * multioutput likelihood WIP * 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> * note and bugfix * add comment * 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. * testing * added QuadratureLikelihood to base, refactored ScalarLikelihood to use it * fix * using the first dimension to hold the quadrature summation * adapting ndiagquad wrapper * merged with gustavocmv/quadrature-change-shape * removed unecessary tf.init_scope * removed print and tf.print * removed print and tf.print * Type annotations Co-authored-by: Vincent Dutordoir <dutordoirv@gmail.com> * Work * Fix test * Remove multioutput from PR * Fix notebook * Add student t test * More tests * Copyright * Removed NDiagGHQuadratureLikelihood class in favor of non-abstract QuadratureLikelihood * _set_latent_and_observation_dimension_eagerly * n_gh ---> num_gauss_hermite_points * removed NDiagGHQuadratureLikelihood from test * black * bugfix * removing NDiagGHQuadratureLikelihood from test * fixed bad commenting * black * refactoring scalar likelihood * adding dtype casts to quadrature * black * small merging fixes * DONE: swap n_gh for num_gauss_hermite_points * black Co-authored-by: ST John <st@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-- <st--@users.noreply.github.com> Co-authored-by: joshuacoales-pio <47976939+joshuacoales-pio@users.noreply.github.com> 15 September 2020, 15:37 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
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
67e583c Fix SGPR upper bound for non zero mean functions (#1560) 10 September 2020, 13:41 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
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
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
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
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
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
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
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
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