| 5c600c7 | Ricardo Vieira | 26 July 2023, 09:31:30 UTC | Use graph_replace instead of clone_replace in VI | 31 July 2023, 08:34:05 UTC |
| 1a06d50 | Ricardo Vieira | 27 July 2023, 11:39:50 UTC | Raise NotImplementedError for multivariate CustomDists | 31 July 2023, 08:34:05 UTC |
| 2303bf9 | Ricardo Vieira | 17 July 2023, 09:02:27 UTC | Bump PyTensor dependency to 2.14.1 | 31 July 2023, 08:34:05 UTC |
| f9e6418 | Ricardo Vieira | 26 July 2023, 09:41:08 UTC | Make test_inference tests fail on unexpected warnings | 31 July 2023, 08:34:05 UTC |
| e3961fc | Dhruvanshu-Joshi | 27 July 2023, 07:58:48 UTC | Logprob derivation for Max (#6769) | 27 July 2023, 07:58:48 UTC |
| 510d3b8 | Daniel Saunders | 26 July 2023, 20:06:26 UTC | Restrict domain on alpha in the CAR distribution (#6801) * Restricted alpha to be greater than -1 and less than 1. Adjusted parameter checks. * Ricardo's suggestions * add tests for code-cov * logp test, test rename, np.all - > np.any | 26 July 2023, 20:06:26 UTC |
| cd1d354 | Michael Osthege | 20 July 2023, 20:38:21 UTC | Mark object stats as `str`-typed | 24 July 2023, 15:06:57 UTC |
| 65eb592 | Michael Osthege | 20 July 2023, 19:23:12 UTC | Fix duplicate `"tune"` stat in McBackend adapter | 24 July 2023, 15:06:57 UTC |
| 38e87e2 | Michael Osthege | 20 July 2023, 19:20:30 UTC | Emit `"tune"` from all stepmethods | 24 July 2023, 15:06:57 UTC |
| 63483b7 | Thomas Wiecki | 22 July 2023, 21:57:22 UTC | ⬆️ UPGRADE: Autoupdate pre-commit config (#6784) * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config --------- Co-authored-by: pymc-bot <pymc-devs@users.noreply.github.com> | 22 July 2023, 21:57:22 UTC |
| 82c6318 | Joe Hall | 19 July 2023, 15:52:50 UTC | Add GP Wrapped Periodic Kernel (#6742) Co-authored-by: Joseph Hall <joseph.hall@bp.com> | 19 July 2023, 15:52:50 UTC |
| 4a65148 | Joe Hall | 19 July 2023, 12:44:30 UTC | GP Covariance Function Type Hints (#6740) Co-authored-by: Joseph Hall <joseph.hall@bp.com> | 19 July 2023, 12:44:30 UTC |
| 42f2e91 | Ricardo Vieira | 17 July 2023, 15:03:30 UTC | Drop support for Python 3.8 | 18 July 2023, 19:09:00 UTC |
| 2269d73 | Ricardo Vieira | 17 July 2023, 07:13:23 UTC | Don't use size and simplify dims example in dimensionality notebook | 17 July 2023, 10:10:28 UTC |
| 6bfbff5 | Daniel Saunders | 12 July 2023, 18:08:32 UTC | Update hyperlinks in GLM core notebook | 13 July 2023, 10:28:23 UTC |
| f8581ab | Ricardo Vieira | 10 July 2023, 12:44:29 UTC | Allow creating CustomDist inside another CustomDist | 12 July 2023, 14:15:01 UTC |
| 13e7c88 | Adriano M. Yoshino | 11 July 2023, 14:47:28 UTC | Fix mathematical notation in conditional_logprob docstrings (#6821) * Fix mathematical notation in conditional_logprob docstrings * Update pymc/logprob/basic.py Accepting change in s. It becomes sigma Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> * Update pymc/logprob/basic.py Accepting change in s. It becomes sigma part 2 Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> * Apply suggestions from code review Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> * s_vv to s2_vv --------- Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> | 11 July 2023, 14:47:28 UTC |
| 8e89828 | Thomas Aarholt | 10 July 2023, 19:52:23 UTC | Prevent unbound trace due to type hints (#6809) * Prevent unbound trace * move enter and exit into metaclass * simpler, a bit more correct approach * add comment | 10 July 2023, 19:52:23 UTC |
| 659f177 | Adriano M. Yoshino | 06 July 2023, 01:59:19 UTC | replacing pytensor-devs for aesara-devs (#6817) * replacing pytensor-devs for aesara-devs * fix typo * Update docs/source/learn/core_notebooks/pymc_pytensor.ipynb Change pytensor hypterlink to "pymc-devs/pytensor" Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> --------- Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> | 06 July 2023, 01:59:19 UTC |
| f67ff8b | Ricardo Vieira | 30 June 2023, 09:54:11 UTC | Use "unobserved" as imputed variable suffix instead of "missing" | 30 June 2023, 17:32:11 UTC |
| 1da28b1 | Ricardo Vieira | 29 June 2023, 13:12:57 UTC | Extend support for automatic imputation | 30 June 2023, 17:32:11 UTC |
| 12de79c | Ricardo Vieira | 29 June 2023, 13:11:16 UTC | Raise informative error when passing masked data to `Data` | 30 June 2023, 17:32:11 UTC |
| cb2c77f | Ricardo Vieira | 05 June 2023, 11:36:09 UTC | Allow non-scalar measurable switch mixtures | 30 June 2023, 09:48:41 UTC |
| 96adf54 | Ricardo Vieira | 30 June 2023, 07:02:14 UTC | Remove unneccessary MeasurableVariable registration | 30 June 2023, 09:48:41 UTC |
| 3577573 | Ricardo Vieira | 30 June 2023, 07:08:59 UTC | Remove unused Model functionality | 30 June 2023, 08:02:24 UTC |
| eb916f0 | Ben Mares | 30 June 2023, 07:40:25 UTC | Fix AePPL copyright notice This seems to be a search/replace mistake | 30 June 2023, 08:01:52 UTC |
| 413af04 | Ricardo Vieira | 29 June 2023, 12:13:04 UTC | Allow check_dist_not_registered to be called inside CustomDist | 29 June 2023, 18:22:20 UTC |
| 4acd5a3 | Ricardo Vieira | 29 June 2023, 12:29:54 UTC | Use less verbose default class_name in `CustomSymbolicDist` | 29 June 2023, 18:22:20 UTC |
| 146afc5 | amyoshino | 28 June 2023, 21:21:51 UTC | adding icdf functions for moyal, gumbel, triangular and weibull | 29 June 2023, 13:16:16 UTC |
| 562fe16 | Ricardo Vieira | 23 June 2023, 14:34:24 UTC | NotImplementedError for icdf of non-injective MeasurableTransforms | 29 June 2023, 12:34:37 UTC |
| 4847914 | David Horsley | 14 June 2023, 07:46:29 UTC | Add lower triangular tags to allow chol rewrites Since pymc-devs/pytensor#303, `cholesky(L.dot(L.T))` will rewritten to L if `L.tag.lower_triangular=True`. This change adds these where appropriate. Fixes #6717. | 29 June 2023, 12:08:06 UTC |
| b76be00 | David Horsley | 14 June 2023, 07:44:29 UTC | Apply rewrites to logp before apply grad This adds safe rewrites to logp before the grad operator is applied. This is motivated by #6717, where expensive `cholesky(L.dot(L.T))` operations are removed. If these remain in the logp graph when the grad is taken, the resulting dlogp graph contains unnecessary operations. However this may improve the stability and performance of grad logp in other situation. | 29 June 2023, 12:08:06 UTC |
| 7b08fc1 | Adriano M. Yoshino | 26 June 2023, 06:07:52 UTC | Add icdf functions for Lognormal, Half Cauchy and Half Normal distributions (#6766) | 26 June 2023, 06:07:52 UTC |
| 14e673f | Maxim Kochurov | 22 June 2023, 11:04:26 UTC | Better coverage for float32 tests (#6780) * create a failing test * fix the bug * simplify * add float32 test to transforms | 22 June 2023, 11:04:26 UTC |
| f91dd1c | Maxim Kochurov | 22 June 2023, 09:35:10 UTC | np.product to np.prod (#6789) | 22 June 2023, 09:35:10 UTC |
| 2806c23 | Ricardo Vieira | 16 June 2023, 05:49:59 UTC | Make tests compatible with latest release of PyTensor | 17 June 2023, 23:05:06 UTC |
| 75ff17a | Oriol Abril-Pla | 17 June 2023, 19:52:13 UTC | speed-up doc building and fix several issues (#6781) * speed-up doc building and fix several issues * undo misc page * try making censored/truncated/simulator nicer * fix methods rubric * fix ref to hide notebook cells | 17 June 2023, 19:52:13 UTC |
| 77f24d7 | Adriano M. Yoshino | 16 June 2023, 07:44:39 UTC | adding icdf function for Cauchy and Logistic with tests (#6747) Co-authored-by: seuabeia <126102654+seuabeia@users.noreply.github.com> | 16 June 2023, 07:44:39 UTC |
| 69514ac | pymc-bot | 12 June 2023, 07:03:20 UTC | ⬆️ UPGRADE: Autoupdate pre-commit config | 16 June 2023, 07:17:39 UTC |
| 8554f6d | Eerik Sven Puudist | 09 June 2023, 23:10:00 UTC | Fix broken link | 16 June 2023, 07:16:12 UTC |
| e69dec9 | Ricardo Vieira | 16 June 2023, 07:05:57 UTC | Simplify Potential docstrings and examples (#6772) * Simplify Potential docstrings and examples Co-authored-by: Bill Engels <w.j.engels@gmail.com> | 16 June 2023, 07:05:57 UTC |
| 9bb3cf0 | Tim Maier | 16 June 2023, 04:31:59 UTC | squeeze dim_0 dimensions for scalars away (#6764) * squeeze dim_0 dimensions for scalars away 1. Squeeze scalars in `xarray.Dataset` generated for `constant_data` by arviz. This is a provisional fix until the behavior of arviz here is refactored. * added test | 16 June 2023, 04:31:59 UTC |
| 53cbcc3 | jaharvey8 | 14 June 2023, 20:45:34 UTC | fixing links to images (#6739) | 14 June 2023, 20:45:34 UTC |
| 9d24a78 | Alejandro Icazatti | 14 June 2023, 20:30:25 UTC | Fix PolyaGamma's docstring (#6672) * Fix typos in PolyaGamma's docstring * Add polyagamma to docs env --------- Co-authored-by: Michael Osthege <michael.osthege@outlook.com> | 14 June 2023, 20:30:25 UTC |
| c792e88 | Luke Lewis-Borrell | 14 June 2023, 06:34:21 UTC | Probabilty inference for arc transformations Co-authored-by: Luke LB <ll17354@bristol.ac.uk> | 14 June 2023, 06:34:21 UTC |
| 154f5b0 | Ricardo Vieira | 08 June 2023, 08:36:48 UTC | Add logprob submodule to API | 12 June 2023, 06:32:59 UTC |
| 951fe52 | Ricardo Vieira | 08 June 2023, 11:36:59 UTC | Rename `warn_missing_rvs` to `warn_rvs` | 12 June 2023, 06:32:59 UTC |
| a579b26 | Ricardo Vieira | 08 June 2023, 08:34:48 UTC | Reorder API entries and remove less useful ones | 12 June 2023, 06:32:59 UTC |
| 07f90e0 | Ricardo Vieira | 08 June 2023, 08:35:03 UTC | Fix docstring header | 12 June 2023, 06:32:59 UTC |
| 0d423b1 | Thomas Wiecki | 11 June 2023, 20:17:12 UTC | Fix missing new-line. | 11 June 2023, 20:17:12 UTC |
| c267293 | Reshama | 11 June 2023, 18:36:08 UTC | rm line at end of file | 11 June 2023, 19:25:33 UTC |
| 63c87e6 | Reshama | 11 June 2023, 18:30:41 UTC | add line at end of file | 11 June 2023, 19:25:33 UTC |
| 9daf113 | Reshama | 11 June 2023, 18:25:45 UTC | add line at end of file | 11 June 2023, 19:25:33 UTC |
| 712c356 | Reshama | 11 June 2023, 18:06:11 UTC | add ODSC sponsor logo to README.rst | 11 June 2023, 19:25:33 UTC |
| 765fdef | Chris Fonnesbeck | 10 June 2023, 15:06:05 UTC | Removed **kwargs from sample_numpyro_nuts and sample_blackjax_nuts (#6768) | 10 June 2023, 15:06:05 UTC |
| 864ecb3 | Ricardo Vieira | 09 June 2023, 14:17:13 UTC | Fix bug in switch mixture logp The True and False branches were being mixed up | 09 June 2023, 14:55:00 UTC |
| 8b5f437 | Ricardo Vieira | 05 June 2023, 10:21:12 UTC | Fix `check_all_tests_are_covered` hook | 08 June 2023, 11:40:56 UTC |
| 2ac88af | Ricardo Vieira | 07 June 2023, 18:00:46 UTC | Rename basic "joint_logprob" functions to "conditional_logp" | 08 June 2023, 08:25:32 UTC |
| a32c5e7 | Joe Hall | 07 June 2023, 15:17:32 UTC | More informative error message for unused step sampler arguments (#6738) Co-authored-by: Joseph Hall <joseph.hall@bp.com> | 07 June 2023, 15:17:32 UTC |
| 261862d | Ricardo Vieira | 05 June 2023, 09:02:34 UTC | Fix auto-naming of multi-output logprobs | 05 June 2023, 19:03:51 UTC |
| 5b68edc | Ricardo Vieira | 05 June 2023, 08:46:34 UTC | Fix nested and single output IfElse logp | 05 June 2023, 19:03:51 UTC |
| a30e0d4 | Ricardo Vieira | 01 June 2023, 07:49:38 UTC | Allow composition of interdependent container variables Join/MakeVector/IfElse can output multiple interdependent variables. These are potentially measurable because in the logp each output is given a distinct value variable. However, this isn't known during the IR rewrites. To circumvent this issue, we run an inner IR rewrite after giving dummy value variables to each output | 05 June 2023, 19:03:51 UTC |
| 9bba026 | Ricardo Vieira | 31 May 2023, 19:04:25 UTC | Fix logprob of `check_and_raise` | 05 June 2023, 19:03:51 UTC |
| 7ed5b71 | Ricardo Vieira | 31 May 2023, 18:28:06 UTC | Cleanup RV in graph checks | 05 June 2023, 19:03:51 UTC |
| 13f9894 | Ricardo Vieira | 31 May 2023, 12:00:48 UTC | New logprob inference logic This commit changes the logic used for logprob inference. Instead of eager bottom-up conversion to measurable variables in the IR rewrites, we only convert nodes whose outputs were marked as "needs_measuring". This is achieved with the new `PreserveRVMappings.request_measurable` method. This strategy obviates the need to undo unnecessary conversions. It also obviates a subtle need for graph cloning via the `ignore_logprob` helper, which prevented intermediate measurable rewrites from being reversed when they were needed to derive the logprob of valued variables, but were not directly valued. This indirect role of `ignore_logprob` is now done more explicitly and efficiently via the `request_measurable` method. All other uses of `ignore_logprob` (and `reconsider_logprob`) were removed from the codebase The `get_measurable_outputs` dispatching was also abandoned in favor of only considering outputs associated with value variables. A new MergeOptimizerRewrite was written to further target local rewrites to only those nodes whose variables have been marked as `needs_measuring`. | 05 June 2023, 19:03:51 UTC |
| 0fa051d | Ricardo Vieira | 01 June 2023, 09:26:04 UTC | Remove unused test util | 05 June 2023, 19:03:51 UTC |
| eb88380 | Geoff Nordling | 01 June 2023, 13:05:05 UTC | uncommented bambi lines | 04 June 2023, 14:13:20 UTC |
| 4d2b2ef | ProCodec | 02 June 2023, 02:19:04 UTC | update installation instructions to request version >5 (#6752) | 02 June 2023, 02:19:04 UTC |
| f3df36b | Thomas Aarholt | 29 May 2023, 18:04:31 UTC | fix tiny error in overload definition | 30 May 2023, 09:42:52 UTC |
| b17a60d | Ricardo Vieira | 29 May 2023, 13:24:49 UTC | Ignore named variables that are not traceable in `get_vars_in_point_list` | 30 May 2023, 09:40:01 UTC |
| fbc62d5 | Ricardo Vieira | 25 May 2023, 12:14:19 UTC | Remove IR `Op`s from final logprob graph | 27 May 2023, 08:33:37 UTC |
| 4d0360c | Ricardo Vieira | 25 May 2023, 12:10:27 UTC | Fix nested replacement of useless IR conversions | 27 May 2023, 08:33:37 UTC |
| 8c93bb5 | Ricardo Vieira | 23 May 2023, 17:20:56 UTC | Fix Minibatch for multiple variables | 24 May 2023, 08:44:44 UTC |
| db15ae4 | Ricardo Vieira | 23 May 2023, 16:04:26 UTC | Avoid cloning of Minibatch values | 24 May 2023, 08:44:44 UTC |
| cafb60b | Ricardo Vieira | 22 May 2023, 13:13:53 UTC | Update PyTensor dependency | 23 May 2023, 08:45:12 UTC |
| bfbc8cc | Ricardo Vieira | 28 April 2023, 13:17:12 UTC | Handle Scan in collect_default_updates This allows proper seeding in CustomDists with Scans | 23 May 2023, 08:32:28 UTC |
| 0073639 | Shreyas Singh | 19 May 2023, 11:48:40 UTC | Remove `joint_logprob` function from `tests.logprob.utils` (#6650) * Remove joint_logprob function from tests.logprob.utils * Move the joint logprob test for subtensors to test_mixture.py | 19 May 2023, 11:48:40 UTC |
| c57769c | Ricardo Vieira | 17 May 2023, 13:56:15 UTC | Rename _replace_rvs_in_graphs and fix bug when replacing input | 17 May 2023, 20:05:22 UTC |
| e1060de | Oriol Abril-Pla | 16 May 2023, 08:14:07 UTC | Add redirects from old v3 notebooks (#6719) * add redirects from old v3 notebooks * fix redirects | 16 May 2023, 08:14:07 UTC |
| bee65b4 | Daniel Saunders | 15 May 2023, 20:14:32 UTC | update gaussian_processes.rst (#6693) * moved and cleaned up GP guide * added GP guide to core_notebooks index * implement oriol's suggestions * implement oriol's suggestions * Update docs/source/learn/core_notebooks/Gaussian_Processes.rst Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * Update docs/source/learn/core_notebooks/Gaussian_Processes.rst Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> | 15 May 2023, 20:14:32 UTC |
| 8f43799 | pymc-bot | 08 May 2023, 07:02:56 UTC | ⬆️ UPGRADE: Autoupdate pre-commit config | 15 May 2023, 08:59:56 UTC |
| 9886f8b | Paul Brown | 08 May 2023, 14:37:24 UTC | Change logger names from all "pymc" to module name (__name__) | 13 May 2023, 13:53:51 UTC |
| f632a34 | Thomas Aarholt | 12 May 2023, 22:42:48 UTC | Type overloading for return_inferencedata in pm.sample() (#6709) | 12 May 2023, 22:42:48 UTC |
| 9b72c2e | James | 06 May 2023, 12:19:40 UTC | Add ICDF function to pareto distribution Adds ICDF (quantile) function for the Pareto distribution. Source https://en.wikipedia.org/wiki/Pareto_distribution Issue #6612 | 11 May 2023, 08:45:02 UTC |
| 10eab32 | James | 06 May 2023, 12:07:32 UTC | Add ICDF function to laplace distribution Adds ICDF (quantile) function for the laplace distribution. Source https://en.wikipedia.org/wiki/Laplace_distribution Issue #6612 | 11 May 2023, 08:45:02 UTC |
| c377bf6 | Reshama Shaikh | 10 May 2023, 17:23:43 UTC | target GLM_linear >> glm_linear (#6714) | 10 May 2023, 17:23:43 UTC |
| a53e865 | Tomas Capretto | 03 May 2023, 14:01:22 UTC | Implement Hurdle distributions | 10 May 2023, 12:02:34 UTC |
| 970db18 | Tomas Capretto | 03 May 2023, 13:57:16 UTC | Move distributions to more consistent places ZeroInflated to mixture.py DiracDelta to distribution.py | 10 May 2023, 12:02:34 UTC |
| 83e3545 | Tomas Capretto | 28 April 2023, 12:46:20 UTC | Remove deprecated Constant alias | 10 May 2023, 12:02:34 UTC |
| 4242faf | Ricardo Vieira | 08 May 2023, 11:39:58 UTC | Speedup Slice sampler | 08 May 2023, 16:04:00 UTC |
| fee9a02 | Ricardo Vieira | 08 May 2023, 11:59:33 UTC | Return tune information from Slice sampler This avoids a crash when mixing slice sampling with another sampler that has `tune` stats | 08 May 2023, 16:04:00 UTC |
| 9e91935 | pymc-bot | 01 May 2023, 07:03:16 UTC | ⬆️ UPGRADE: Autoupdate pre-commit config | 07 May 2023, 19:28:31 UTC |
| a617bf2 | Manul Patel | 28 April 2023, 14:48:31 UTC | Added scale parameterization to `Exponential` (#6677) | 28 April 2023, 14:48:31 UTC |
| 371472d | Shreyas Singh | 28 April 2023, 10:50:45 UTC | Add logprob inference for not operations (#6689) | 28 April 2023, 10:50:45 UTC |
| d4bb701 | Luke Lewis-Borrell | 28 April 2023, 09:44:16 UTC | Derive logprob for hyperbolic and error transformations (#6664) * cleaned up if block in find_measurable_transform * Adapt default `RVTransform.log_jac_det` to univariate and vector transformations. * Use np.testing in check_jacobian_det Co-authored-by: Luke LB <ll17354@bristol.ac.uk> Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> | 28 April 2023, 09:44:16 UTC |
| 890c2cc | Manul Patel | 26 April 2023, 17:20:42 UTC | Updated Pytest video series link | 28 April 2023, 08:29:15 UTC |
| 5cf7efe | Gokul D | 13 April 2023, 19:11:47 UTC | Fix numerical precision issues in discrete ICDFs. | 27 April 2023, 15:29:51 UTC |
| 910d9ef | Shreyas Singh | 27 April 2023, 12:07:46 UTC | Add logcdf implementation for Truncated distributions (#6690) | 27 April 2023, 12:07:46 UTC |
| 9f01be2 | Dhruvanshu-Joshi | 26 April 2023, 17:32:49 UTC | Rectify type-hints for `set_data` | 26 April 2023, 17:32:49 UTC |
| a86fe7c | David Horsley | 26 April 2023, 17:24:39 UTC | Fix WhiteNoise subclassing from Covariance (#6674) * fix WhiteNoise subclassing from Covariance (#6673) Since #6458, Covariance is now the base class for kernels/covariance functions with input_dim and active_dims, which does not include WhiteNoise and Constant kernels. * add regression test for #6673 * fix WhiteNoise input to marginal GP | 26 April 2023, 17:24:39 UTC |
