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Revision Author Date Message Commit Date
9f01be2 Rectify type-hints for `set_data` 26 April 2023, 17:32:49 UTC
a86fe7c 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 Make logprob inference for binary ops independent of order of inputs (#6682) 26 April 2023, 13:21:11 UTC
a59c9cd Adding book cover page image into the documentation page. 21 April 2023, 10:58:16 UTC
3f7881e update link to pymc port of DBDA code 20 April 2023, 06:50:09 UTC
61be336 Add logprob derivation for >= and <= operations 19 April 2023, 17:42:01 UTC
9b712bf Derive logprob of less and greater than comparisons (#6662) 19 April 2023, 11:53:59 UTC
f2bb88b 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 Allow logcdf inference in CustomDist 15 April 2023, 05:10:22 UTC
e2eb26d 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 Arrange distributions and sub-contents alphabetically (#6653) 13 April 2023, 11:29:47 UTC
23572e1 Fix dtype casting bug in icdf function 13 April 2023, 11:21:36 UTC
fa82fef 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 Bump Pytensor dependency 12 April 2023, 08:54:36 UTC
5d68bf3 Fix changed files filters in tests workflow Introduced in 433703ab0156c88de4eb3b180ea85ec21dd3e3fb 08 April 2023, 11:44:14 UTC
0d7413e Add all_tests job to be used as single requirement 07 April 2023, 13:47:04 UTC
7973967 Add Type Hints to distribution parameters (#6635) 07 April 2023, 13:15:48 UTC
09dc9d0 Raise warning if RVs are present in derived probability graphs 06 April 2023, 19:16:46 UTC
30c9179 Improve docstrings in GP module (#6652) 06 April 2023, 15:56:59 UTC
e5a200f 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 Add timestamps to list of possible contributions (#6623) 06 April 2023, 14:08:39 UTC
041e2f9 Add Gitpod video to contributing page (#6646) 06 April 2023, 13:10:27 UTC
48c8dc8 ⬆️ UPGRADE: Autoupdate pre-commit config 04 April 2023, 19:34:33 UTC
264afdc ⬆️ 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 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 fix docstrings for censored and timeseries (#6638) 01 April 2023, 09:00:33 UTC
617f93c install theme from conda (#6639) 01 April 2023, 08:59:38 UTC
8d5b236 update links to sponsor images 31 March 2023, 22:53:19 UTC
6404805 Add model debug helper 31 March 2023, 14:36:03 UTC
4c64eb9 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 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 Add rtd preview action 30 March 2023, 09:02:47 UTC
1bfd128 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 Allow logcdf and icdf inference 30 March 2023, 08:43:50 UTC
ae9fcac Implemented logprob for SpecifyShape and CheckandRaise (#6538) 29 March 2023, 21:02:37 UTC
f7861b5 Updating Error message when checking the starting values for MCMC (#6632) 29 March 2023, 20:50:23 UTC
f3ce16f Infer logp for elemwise transformations of multivariate variables 29 March 2023, 10:49:11 UTC
d860f63 Fix broadcasting issue in ScaleTransform jacobian 29 March 2023, 10:49:11 UTC
6f80846 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 Do mamba and pre-commit updates in background 25 March 2023, 19:02:35 UTC
be560e4 Define PRE_COMMIT_HOME in dev.Dockerfile 25 March 2023, 19:02:35 UTC
3f4dc72 Bump dev container base image 25 March 2023, 19:02:35 UTC
9a3f504 Separate logp-related dispatch helpers from user facing functions 25 March 2023, 17:28:55 UTC
d1625da Simplify single variable logp inference 25 March 2023, 17:28:55 UTC
a584d98 Rename logprob/joint_logprob to logprob/basic.py 25 March 2023, 17:28:55 UTC
2fcce43 Added ICDF for the discrete uniform distribution. 24 March 2023, 06:32:52 UTC
067d89b 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 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 Fix a typo in the docstring of OderedLogistic (#6611) 18 March 2023, 08:20:45 UTC
c7279b5 Remove shape functions (#6556) 17 March 2023, 15:38:56 UTC
0334994 Derive logprob of IfElse graphs 17 March 2023, 12:13:39 UTC
239da11 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 Fix logprob inference for scans with carried deterministic states 16 March 2023, 13:14:02 UTC
a542581 Add test for scans over sequences 16 March 2023, 13:14:02 UTC
fafc020 Use better `assert_no_rvs` from logprob submodule This utility can find RVs in inner graphs 16 March 2023, 13:14:02 UTC
bae121a 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 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
9836d00 Refactor utility to ignore the logprob of multiple variables while keeping their interdependencies intact 13 March 2023, 21:43:19 UTC
1cc9863 Use more readable `ignore_logprob` helper in logprob submodule 13 March 2023, 21:43:19 UTC
0bda194 Renamed aliases from at to pt 13 March 2023, 21:26:54 UTC
19d8bfe Fix release yml 13 March 2023, 20:57:59 UTC
4da5edf Implement `check_icdf` helper to test icdf implementations Note that adding a nan switch to the icdf expression of discrete variables, prevents the returned dtype to be the same as the original distribution. There is no integer nan! 13 March 2023, 19:58:34 UTC
f043ad9 Add flag to `CheckParameterValue` to inform whether it can be replaced by -inf 13 March 2023, 19:58:34 UTC
5becc49 Simplify `check_logp` and related testing helpers 13 March 2023, 19:58:34 UTC
f63268f Do not test invalid parameter combinations 13 March 2023, 19:58:34 UTC
312bde4 ⬆️ UPGRADE: Autoupdate pre-commit config 13 March 2023, 18:51:41 UTC
457421b Fix trailing whitespace. 13 March 2023, 12:01:17 UTC
da68d11 Add nuts_sampler_kwargs and nuts_kwargs to pm.sample (#6581) * Reinstate nuts_kwargs in sample for passing arguments to numpyro * Removed redundant condition from if statement * Added sampler_kwargs * Rename sampler_kwargs; fix test failures * Ensure nuts_kwargs get passed to pymc nuts * Fix test_step_args failure * Moved numpyro test; use nuts_sampler_kwargs * Test failure fix * Fix docstrings for nuts/sampler kwargs; debugging target accept argument passing * Removed passing kwargs to external samplers; only nuts_sampler_kwargs for clarity * Revert nuts_kwargs to nuts * Fix failures in test_mcmc_external * Revert argument parameterization * Update pymc/sampling/mcmc.py Apply suggested nuts_sampler_kwarg docstring change Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> --------- Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> 12 March 2023, 18:32:33 UTC
ff8a4c7 Fix `warn_treedepth` looking at the wrong stat (#6591) * Fix `warn_treedepth` looking at the wrong stat * Add test for `warn_treedepth` function Closes #6587 12 March 2023, 14:24:33 UTC
b6521f2 Add Mistplay sponsor (#6570) * Adding Mistplay image in the Readme * Adding Mistplay image in the Readme 11 March 2023, 13:40:16 UTC
5392336 fix typo 11 March 2023, 13:07:00 UTC
fc51fd3 Fix typos in Potential docstring * Remove spurious minus signs from the first two code examples in the Potential function * Shorten warning about applicability of Potential only to logp-based sampling 11 March 2023, 12:22:26 UTC
5603792 Add explicit support for Python 3.11 10 March 2023, 18:33:51 UTC
4965292 Skip test_polyagamma_moment if library is not installed 10 March 2023, 18:33:51 UTC
cf6d4ce Allow passing dims to Potential and Deterministic (#6576) * Adding dims parameter in Potential * Test case to check the dims in potential 10 March 2023, 16:59:56 UTC
047141c Gitpod instructions (#6549) * initial gitpod instructions * update url * spelling * more instructions on gitpod * new line at end of file * fix trailing whitespace * fix trailing whitespace * fix trailing whitespace * fix wording * try image * try sphinx image code * add link format * add link format * add link format * add link format * try html for image Co-authored-by: Ben Mares <services-git-throwaway1@tensorial.com> * add blank line * try image code * spacing, fix commit errors * backticks * try image option again * terminal instructions * clarify instructions * fix image agai * fix precommit spacing errors * try admonition * try double indent * resize image * pre-commit error * add workspace image * clean up formatting * fix pre-commit error * fix pre-commit error * pre-commit error * use generic user name Co-authored-by: Ben Mares <services-git-throwaway1@tensorial.com> * indent note Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * use console instead of bash for backticks content Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * indent list Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * verb grammar * use console instead of bash * clean up text * clean up text and formatting * indent * indent --------- Co-authored-by: Ben Mares <services-git-throwaway1@tensorial.com> Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> 09 March 2023, 10:59:57 UTC
a41d524 Bring back testing utilities used in downstream packages Follow up to * 534a9ae28a6bfea3bc31921cd92e4e4d2875b6c9 * e1d36cacb2cfb946f56872ee03e8678dc6ccf7f4 08 March 2023, 13:26:08 UTC
49aacf4 Allow Scan logprob inference of non-pure RandomVariable outputs Most of the IR logprob rewrites require a PreserveRVMappings feature in the fgraph. The rewrite responsible to introduce IR in the inner graph of Scan was not adding this feature. In addition, find_measurable_scans, was bailing out when there were MesurableVariable nodes that were not outputs, even if these were being used by downstream nodes as the source of measurability. 08 March 2023, 09:26:11 UTC
e76bba9 Fix bug in transform_scan_values 07 March 2023, 17:46:20 UTC
534a9ae Exclude tests from package discovery (#6552) * Clean up MANIFEST.in * Remove useless option from setup.py * Exclude tests from package discovery * Make get_data not look at local files anymore This seems to be a relic of the past when `tests/data` contained data files. It is not the case anymore. 07 March 2023, 07:43:55 UTC
b57cabe ⬆️ UPGRADE: Autoupdate pre-commit config 06 March 2023, 19:55:02 UTC
8208291 changed params after sigma to kwarg only 06 March 2023, 11:34:25 UTC
fb83972 Fix no-commit-to-branch pre-commit hook to protect main 05 March 2023, 22:10:54 UTC
253aaa8 Updated docstring for Potential function (#6559) * Updated docstring for Potential function * Updating docstring according to suggestions * Updated Potential docstring as per suggestion 05 March 2023, 20:24:55 UTC
2f945bb Revert "Default to using McBackend" This reverts commit 1988b6581b2ec35898e0864fb2ccac51c40f91ad. 02 March 2023, 18:47:25 UTC
1988b65 Default to using McBackend 01 March 2023, 09:32:38 UTC
5510d3f Test McBackend support 01 March 2023, 09:32:38 UTC
76df402 Add optional McBackend support 01 March 2023, 09:32:38 UTC
6a0e74d Refactor `StatsBijection` to expose information about object stats 01 March 2023, 09:32:38 UTC
763a3ea Do not install nutpie for external sampler tests Conda nutpie, and soon pip, depend on the last release of PyMC and by association PyTensor, leading to dependency issues when trying to test compatibility after PyMC bumps the PyTensor dependency. 28 February 2023, 15:57:16 UTC
5bf1bb7 Remove type hint workaround Was fixed in https://github.com/pymc-devs/pytensor/pull/205 28 February 2023, 15:57:16 UTC
5d9f72c Bump PyTensor dependency to 2.10.1 28 February 2023, 15:57:16 UTC
1ca1c94 Replace rvs_to_total_sizes mapping by ManibatchRandomVariables 28 February 2023, 13:06:13 UTC
33d641d Fix two typos. 27 February 2023, 00:10:38 UTC
14a10b7 Refactor sample return (#6546) * Extract return part of `pm.sample` * Speed up `test_mcmc` * Group tests related to `pm.sample` return parameters * Consolidate tests of return options Removes a regression test added in #3821 because it took 14 seconds. 26 February 2023, 10:50:25 UTC
9b59771 Add check for variables in step samplers (#6524) * added value check for step samplers * changing error message to be more informative * added test checking if variable not being in model.value_vars will trigger Value error * implemented changes from PR review * Fix rebase --------- Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 25 February 2023, 16:11:30 UTC
b9a3dcc Fix some code lints found with ruff (#6545) * Make isort happy with imports order * Avoid shadowing the logprob fn with a local name * Deal with unused error names * Remove unreachable return * Remove unread variable * Fix type checking for variational/approximations * A few typing fixes 25 February 2023, 11:13:30 UTC
e1d36ca Move tests outside of code directory 22 February 2023, 22:10:01 UTC
562e51e issue #5791, dims & cords inference from xarray (#6514) * added dim inference from xarray, deprecation warning and unittest for the new feature * fixed typo in warning * fixed accidental quotation around dim * fixed failing assertions * found and fixed cause of the failing test * changed the coords assertion according to suggested form * fixing mypy type missmatch * working on getting the test to work * removed typecasting to string on dim_name, was causing the mypy to fail * took care locally of mypy errors * Typo/formatting fixes --------- Co-authored-by: Michal Raczycki <michalraczycki@macbook-pro-michal.home> Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 22 February 2023, 16:51:14 UTC
e45e6c2 increase zerosum readability issue #6459 (#6522) * added n_zerosum_axes and added backwards compatibility for previous parameter name * fixed typo that caused the zerosum_axes param not to be saved correctly in the new param * adapted tests to use n_zerosum_axes --------- Co-authored-by: Michal Raczycki <michalraczycki@macbook-pro-michal.home> 22 February 2023, 10:14:14 UTC
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