| 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 |
| 55d915c | Shreyas Singh | 26 April 2023, 13:21:11 UTC | Make logprob inference for binary ops independent of order of inputs (#6682) | 26 April 2023, 13:21:11 UTC |
| a59c9cd | Sundarapandiyan | 21 April 2023, 10:38:14 UTC | Adding book cover page image into the documentation page. | 21 April 2023, 10:58:16 UTC |
| 3f7881e | Christian Luhmann | 20 April 2023, 03:55:35 UTC | update link to pymc port of DBDA code | 20 April 2023, 06:50:09 UTC |
| 61be336 | shreyas3156 | 19 April 2023, 10:37:00 UTC | Add logprob derivation for >= and <= operations | 19 April 2023, 17:42:01 UTC |
| 9b712bf | Shreyas Singh | 19 April 2023, 11:53:59 UTC | Derive logprob of less and greater than comparisons (#6662) | 19 April 2023, 11:53:59 UTC |
| f2bb88b | Ricardo Vieira | 17 April 2023, 14:52:50 UTC | Make metropolis elemwise updates independent of each other Not updating q0 after each elemwise update rendered subsequent proposals dependent on the previous ones. | 19 April 2023, 07:34:01 UTC |
| 1ed4475 | Ricardo Vieira | 13 April 2023, 07:53:27 UTC | Allow logcdf inference in CustomDist | 15 April 2023, 05:10:22 UTC |
| e2eb26d | Ricardo Vieira | 30 March 2023, 17:59:56 UTC | Do not require class_name for CustomDist and Simulator dists * Also remove the experimental warning when using CustomSymbolicDists | 15 April 2023, 05:10:22 UTC |
| aae97a2 | Dhruvanshu-Joshi | 13 April 2023, 11:29:47 UTC | Arrange distributions and sub-contents alphabetically (#6653) | 13 April 2023, 11:29:47 UTC |
| 23572e1 | Ricardo Vieira | 13 April 2023, 08:29:07 UTC | Fix dtype casting bug in icdf function | 13 April 2023, 11:21:36 UTC |
| fa82fef | Dhruvanshu-Joshi | 13 April 2023, 10:44:49 UTC | Fix bug in random function of HalfStudent (#6658) Co-authored-by: Ricardo Vieira <ricardo.vieira1994@gmail.com> | 13 April 2023, 10:44:49 UTC |
| 2a324bc | Ricardo Vieira | 11 April 2023, 13:15:00 UTC | Bump Pytensor dependency | 12 April 2023, 08:54:36 UTC |
| 5d68bf3 | Ricardo Vieira | 08 April 2023, 06:25:58 UTC | Fix changed files filters in tests workflow Introduced in 433703ab0156c88de4eb3b180ea85ec21dd3e3fb | 08 April 2023, 11:44:14 UTC |
| 0d7413e | Ricardo Vieira | 07 April 2023, 06:36:53 UTC | Add all_tests job to be used as single requirement | 07 April 2023, 13:47:04 UTC |
| 7973967 | Prince Takyi | 07 April 2023, 13:15:48 UTC | Add Type Hints to distribution parameters (#6635) | 07 April 2023, 13:15:48 UTC |
| 09dc9d0 | Ricardo Vieira | 05 April 2023, 09:34:18 UTC | Raise warning if RVs are present in derived probability graphs | 06 April 2023, 19:16:46 UTC |
| 30c9179 | Daniel Saunders | 06 April 2023, 15:56:59 UTC | Improve docstrings in GP module (#6652) | 06 April 2023, 15:56:59 UTC |
| e5a200f | Reshama Shaikh | 06 April 2023, 14:21:07 UTC | Add welcome bot (#6602) * config.yml file >>> add welcome bot links * Update links to contributing guide --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> | 06 April 2023, 14:21:07 UTC |
| b1a75ae | Reshama Shaikh | 06 April 2023, 14:08:39 UTC | Add timestamps to list of possible contributions (#6623) | 06 April 2023, 14:08:39 UTC |
| 041e2f9 | Reshama Shaikh | 06 April 2023, 13:10:27 UTC | Add Gitpod video to contributing page (#6646) | 06 April 2023, 13:10:27 UTC |
| 48c8dc8 | pymc-bot | 03 April 2023, 07:03:48 UTC | ⬆️ UPGRADE: Autoupdate pre-commit config | 04 April 2023, 19:34:33 UTC |
| 264afdc | Thomas Wiecki | 02 April 2023, 21:51:00 UTC | ⬆️ UPGRADE: Autoupdate pre-commit config (#6624) * ⬆️ UPGRADE: Autoupdate pre-commit config --------- Co-authored-by: pymc-bot <pymc-devs@users.noreply.github.com> | 02 April 2023, 21:51:00 UTC |
| b7764dd | gokuld | 01 April 2023, 18:37:28 UTC | Added ICDF for the continuous exponential distribution. (#6641) * Added ICDF for the continuous exponential distribution. * Removed redundant out of bounds parameter tests. | 01 April 2023, 18:37:28 UTC |
| eb4e353 | Adrien | 01 April 2023, 09:00:33 UTC | fix docstrings for censored and timeseries (#6638) | 01 April 2023, 09:00:33 UTC |
| 617f93c | Oriol Abril-Pla | 01 April 2023, 08:59:38 UTC | install theme from conda (#6639) | 01 April 2023, 08:59:38 UTC |
| 8d5b236 | reshamas | 31 March 2023, 21:40:27 UTC | update links to sponsor images | 31 March 2023, 22:53:19 UTC |
| 6404805 | Ricardo Vieira | 30 March 2023, 13:54:09 UTC | Add model debug helper | 31 March 2023, 14:36:03 UTC |
| 4c64eb9 | Ricardo Vieira | 30 March 2023, 13:34:54 UTC | Don't use `check_parameters` in `get_tau_sigma`. The default use of `check_parameters` indicates that an expression can be replaced by -inf, if the constraints aren't met. Instead, if `can_be_replaced_by_ninf=False`, sampling would fail for negative tau/sigma. To avoid this, the conversion now returns the right value for positive tau or sigma, but negative images if the inputs were negative. The methods that then validate the paramters (such as logp, logcdf, random), can later catch this. | 31 March 2023, 14:36:03 UTC |
| 3f2a1da | Ricardo Vieira | 03 March 2023, 12:02:32 UTC | Improve collect_default_updates * It works with nested RNGs * It raises error if RNG used in SymbolicRandomVariable is not given an update * It raises warning if same RNG is used in multiple nodes | 30 March 2023, 10:21:00 UTC |
| a75af50 | Oriol Abril-Pla | 29 March 2023, 12:08:48 UTC | Add rtd preview action | 30 March 2023, 09:02:47 UTC |
| 1bfd128 | Oriol Abril-Pla | 29 March 2023, 12:07:29 UTC | Install theme from pypi Also updates the sphinx cap to match the one from the theme, which is more realistic. I haven't tried but doubt our doc build would still work with sphinx 1.5 | 30 March 2023, 09:02:47 UTC |
| 46f8e2f | Ricardo Vieira | 13 March 2023, 20:17:45 UTC | Allow logcdf and icdf inference | 30 March 2023, 08:43:50 UTC |
| ae9fcac | Dhruvanshu-Joshi | 29 March 2023, 21:02:37 UTC | Implemented logprob for SpecifyShape and CheckandRaise (#6538) | 29 March 2023, 21:02:37 UTC |
| f7861b5 | Dhruvanshu-Joshi | 29 March 2023, 20:50:23 UTC | Updating Error message when checking the starting values for MCMC (#6632) | 29 March 2023, 20:50:23 UTC |
| f3ce16f | Ricardo Vieira | 17 March 2023, 16:39:28 UTC | Infer logp for elemwise transformations of multivariate variables | 29 March 2023, 10:49:11 UTC |
| d860f63 | Ricardo Vieira | 20 March 2023, 15:43:24 UTC | Fix broadcasting issue in ScaleTransform jacobian | 29 March 2023, 10:49:11 UTC |
| 6f80846 | Ricardo Vieira | 20 March 2023, 15:45:38 UTC | Fix jacobian dimensionality alignment in ChainedTransform The existing code only considered mixing of scalar and vector transforms, but not potentially higher dimensionality transforms (e.g., matrix) | 29 March 2023, 10:49:11 UTC |
| 83cd926 | Ben Mares | 23 March 2023, 22:31:43 UTC | Do mamba and pre-commit updates in background | 25 March 2023, 19:02:35 UTC |
| be560e4 | Ben Mares | 23 March 2023, 21:46:33 UTC | Define PRE_COMMIT_HOME in dev.Dockerfile | 25 March 2023, 19:02:35 UTC |
| 3f4dc72 | Ben Mares | 23 March 2023, 21:44:46 UTC | Bump dev container base image | 25 March 2023, 19:02:35 UTC |
| 9a3f504 | Ricardo Vieira | 13 March 2023, 17:58:13 UTC | Separate logp-related dispatch helpers from user facing functions | 25 March 2023, 17:28:55 UTC |
| d1625da | Ricardo Vieira | 13 March 2023, 17:03:31 UTC | Simplify single variable logp inference | 25 March 2023, 17:28:55 UTC |
| a584d98 | Ricardo Vieira | 13 March 2023, 16:55:19 UTC | Rename logprob/joint_logprob to logprob/basic.py | 25 March 2023, 17:28:55 UTC |
| 2fcce43 | Gokul D | 23 March 2023, 10:55:12 UTC | Added ICDF for the discrete uniform distribution. | 24 March 2023, 06:32:52 UTC |
| 067d89b | Chris Fonnesbeck | 22 March 2023, 22:51:18 UTC | Improved docstring for predictions argument in sample_posterior_predictive (#6616) * Improved docstring for predictions argument in sample_posterior_predictive * Fix typos Co-authored-by: Ravin Kumar <7213793+canyon289@users.noreply.github.com> --------- Co-authored-by: Ravin Kumar <7213793+canyon289@users.noreply.github.com> | 22 March 2023, 22:51:18 UTC |
| 473c952 | Michal Raczycki | 19 March 2023, 15:28:37 UTC | Implement icdf for Univariate distribution (#6528) Also extended testing.check_icdf with skip_paradomain_outside_edge_test param --------- Co-authored-by: Michal Raczycki <michalraczycki@macbook-pro-michal.home> | 19 March 2023, 15:28:37 UTC |
| 67925df | Nathaniel | 18 March 2023, 08:20:45 UTC | Fix a typo in the docstring of OderedLogistic (#6611) | 18 March 2023, 08:20:45 UTC |
| c7279b5 | Sandra Yojana Meneses | 17 March 2023, 15:38:56 UTC | Remove shape functions (#6556) | 17 March 2023, 15:38:56 UTC |
| 0334994 | Ricardo Vieira | 16 February 2023, 16:25:59 UTC | Derive logprob of IfElse graphs | 17 March 2023, 12:13:39 UTC |
| 239da11 | Johannes Keyser | 17 March 2023, 11:24:26 UTC | Add definition of B in documentation for Beta distribution (#6604) * Add definition of B in documentation for Beta dist * Define B in Beta distribution and link Wikipedia. | 17 March 2023, 11:24:26 UTC |
| 5dcd101 | Ricardo Vieira | 08 March 2023, 15:07:12 UTC | Fix logprob inference for scans with carried deterministic states | 16 March 2023, 13:14:02 UTC |
| a542581 | Ricardo Vieira | 08 March 2023, 15:03:31 UTC | Add test for scans over sequences | 16 March 2023, 13:14:02 UTC |
| fafc020 | Ricardo Vieira | 08 March 2023, 14:06:22 UTC | Use better `assert_no_rvs` from logprob submodule This utility can find RVs in inner graphs | 16 March 2023, 13:14:02 UTC |
| bae121a | Bill Engels | 14 March 2023, 23:05:15 UTC | Add HSGP Latent GP approximation (#6458) * add HSGP implementation * Extend Covariances to support power spectral densities --------- Co-authored-by: Michael Osthege <michael.osthege@outlook.com> | 14 March 2023, 23:05:15 UTC |
| c709abf | Shreyas Singh | 14 March 2023, 09:42:17 UTC | Remove `auto` argument from `pm.Deterministic` docstring (#6592) * Remove auto argument from Deterministic * Add missing arguments in the deterministic docstring as per numpydoc style guide * Add missing arguments in the Potential docstring * Add spaces around colons --------- Co-authored-by: Michael Osthege <michael.osthege@outlook.com> | 14 March 2023, 09:42:17 UTC |
