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23e418d Implement `default_transform` and `transform` argument for distributions (#7207) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 19 April 2024, 07:27:25 UTC
ed62da1 Add introduction section to Transformations API page to document role of Transforms (#7232) 19 April 2024, 07:24:57 UTC
4bc8439 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7) 16 April 2024, 16:14:35 UTC
08dea8f Fix gradient bug in models with max operation 16 April 2024, 16:14:20 UTC
f90e44f Temporarily pin Scipy in JAX job 15 April 2024, 13:39:13 UTC
34c2d31 Bump docker/setup-buildx-action from 3.2.0 to 3.3.0 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.2.0 to 3.3.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v3.2.0...v3.3.0) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 15 April 2024, 04:05:52 UTC
f3c3086 Reimplement several RandomVariables as SymbolicRandomVariables This allows sampling from multiple backends without having to dispatch for each one 14 April 2024, 05:16:48 UTC
9d4a3d7 Tweaks to SymbolicRandomVariables * Allow signature to handle rng and size arguments explicitly. * Parse ndim_supp and ndims_params from class signature * Move rv_op method to the SymbolicRandomVariable class and get rid of dummy inputs logic (it was needed in previous versions of PyTensor) * Fix errors in automatic signature of CustomDist * Allow dispatch methods without filtering of inputs for SymbolicRandomVariable distributions 14 April 2024, 05:16:48 UTC
d81473f Remove wrong instantiation from test This is not only not used anywhere, but could also try to initiate an RV with incompatible shapes and size 14 April 2024, 05:16:48 UTC
4211a39 Replace CData with Data in model grpah 14 April 2024, 05:14:59 UTC
6073d8d Fix bug in `compute_deterministics` 12 April 2024, 16:26:35 UTC
7ffd47d [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0) - [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5) 12 April 2024, 07:06:11 UTC
0a4ae15 Fix DOI visibility badge in README In README file in .rst format, some badges from Shields.io on Github may require a ".svg" in the path 09 April 2024, 14:50:25 UTC
5f95fc2 Allow Truncation of CustomDists 08 April 2024, 17:01:11 UTC
1195261 Manage SharedVariables explicitly in SymbolicRandomVariable 08 April 2024, 17:01:11 UTC
f0390d4 Automatically retrieve updates from OpFromGraph nodes 08 April 2024, 17:01:11 UTC
937e5fd Fix join logp for multivariate RVs 08 April 2024, 12:35:51 UTC
6f90f83 fix TensorVariable typo in CustomDist 08 April 2024, 09:35:58 UTC
65f0b1e Update docs/source/contributing/developer_guide.md Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> 06 April 2024, 13:09:56 UTC
424ece0 Fix link and typo in developer_guide.md Fix link to `MH-sampler`'s `astep()` method. 06 April 2024, 13:09:56 UTC
9fd90c0 document sampling related functions as users should import them 06 April 2024, 11:11:25 UTC
3d3a4fd Add utility to compute deterministics 06 April 2024, 11:11:25 UTC
ac12dcd Refactor utility to apply a PointFunc over a dataset 06 April 2024, 11:11:25 UTC
ce24ff1 Move dataset_to_point_list to arviz module 06 April 2024, 11:11:25 UTC
443b6ed Overload return type of compile_fn 06 April 2024, 11:11:25 UTC
bd74474 Bump mypy target python version 05 April 2024, 13:40:45 UTC
b48f80d Fix RUF007 (itertools.pairwise) 05 April 2024, 13:40:45 UTC
6da7db5 Fix UP007 (Typealias Unions and Optionals) 05 April 2024, 13:40:45 UTC
7bb6bf8 Fix UP038 (isinstance(..., X | Y)) 05 April 2024, 13:40:45 UTC
2a86c6b Apply safe ruff fixes 05 April 2024, 13:40:45 UTC
6955631 Bump PyTensor version and drop Python 3.9 05 April 2024, 13:40:45 UTC
034b9a4 Make default STEP_METHODS a list that can be modified 05 April 2024, 11:55:48 UTC
22e8f0b Replace fastprogress progress bars with rich (#7233) * Replace fastprogress with rich * Bugfixes for ADVI progress bars * Bugfixes for MAP progress bars * Fixed final update to progress bar * SMC progress bar working * Fixes to MAP progress bar * Customize progress bar theme * Added progressbar_theme argument * Moved default progressbar theme to util * Convert compute_log_density to use Progress instead of track * Getting rid of mypy complaint 03 April 2024, 18:15:35 UTC
207821d Implement model transform that freezes RV dims and Data 03 April 2024, 11:20:55 UTC
1ffbc2c Make coords and data always mutable 03 April 2024, 11:20:55 UTC
9f15330 Allow defining mode from compile_* functions 03 April 2024, 11:20:55 UTC
d8816c7 Add graphic for contributors. 31 March 2024, 12:33:42 UTC
e442348 Add HSGPPeriodic to Docs 29 March 2024, 09:15:31 UTC
4f6831e use ive for numerical stability (#7228) 29 March 2024, 00:05:11 UTC
120fc4e Improve example on expanded sample_posterior_predictive Sample posterior_predictive relies on other groups to infer volatility, so it's important to keep the whole InferenceData. Also there's a shape error if `sample_dims` is not specified 27 March 2024, 21:30:46 UTC
81d31c8 List more math function in API docs (#7211) Also removes deprecated functions and deprecates numpy helpers Co-authored-by: Ricardo Vieira <ricardo.vieira1994@gmail.com> 27 March 2024, 09:30:57 UTC
89f6fcf [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4) 25 March 2024, 19:19:23 UTC
4c3ec36 Add var_names argument to sample (#7206) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 25 March 2024, 18:46:27 UTC
cdfa8c0 add _moment function for bacward backward compatibility (#7216) 25 March 2024, 18:37:41 UTC
abe7bc9 fixing check_parameters occurences in icdf functions, replacing with check_icdf_parameters 25 March 2024, 09:55:44 UTC
f302882 Add icdf functions for Beta, Gamma, Chisquared and Students distributions removing unnecessary parameterization test on studentT test removing unnecessary test on chisquared test 25 March 2024, 09:55:44 UTC
3841c7b Remove unused comp_shape from NormalMixture 25 March 2024, 09:37:49 UTC
a033261 Codecov reintroduce after_n_builds 22 March 2024, 15:55:14 UTC
61ce412 Remove filter for solved warning 22 March 2024, 11:13:36 UTC
20e4722 Ignore DeprecationWarning triggered by arviz 22 March 2024, 11:13:36 UTC
b4412d1 Test on Python 3.12 22 March 2024, 11:13:36 UTC
89b1985 Bump PyTensor dependency 22 March 2024, 11:13:36 UTC
4c0d838 Specify python_version for mypy 22 March 2024, 10:23:09 UTC
06acd99 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.2...v0.3.3) 22 March 2024, 10:23:09 UTC
b983e33 Bump docker/setup-buildx-action from 3.1.0 to 3.2.0 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.1.0 to 3.2.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v3.1.0...v3.2.0) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 22 March 2024, 10:15:16 UTC
cb51389 Bump docker/login-action from 3.0.0 to 3.1.0 Bumps [docker/login-action](https://github.com/docker/login-action) from 3.0.0 to 3.1.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/343f7c4344506bcbf9b4de18042ae17996df046d...e92390c5fb421da1463c202d546fed0ec5c39f20) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 22 March 2024, 10:13:13 UTC
201a5b2 Bump docker/build-push-action from 5.2.0 to 5.3.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5.2.0 to 5.3.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/af5a7ed5ba88268d5278f7203fb52cd833f66d6e...2cdde995de11925a030ce8070c3d77a52ffcf1c0) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 22 March 2024, 10:02:12 UTC
6b850a5 Bump actions/checkout from 4.1.1 to 4.1.2 Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.1 to 4.1.2. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/b4ffde65f46336ab88eb53be808477a3936bae11...9bb56186c3b09b4f86b1c65136769dd318469633) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> 22 March 2024, 10:01:25 UTC
aa679f3 Add `print_name` to Truncated and CustomDists 21 March 2024, 14:01:44 UTC
30d00fe Fix expression for the variance in ZINB docstring 18 March 2024, 14:31:33 UTC
a06081e Improve docs 13 March 2024, 09:33:17 UTC
509b6b5 Bump docker/build-push-action from 5.0.0 to 5.2.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5.0.0 to 5.2.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/0565240e2d4ab88bba5387d719585280857ece09...af5a7ed5ba88268d5278f7203fb52cd833f66d6e) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 13 March 2024, 09:30:40 UTC
5d4f469 [pre-commit.ci] pre-commit autoupdate (#7191) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.2) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> 13 March 2024, 09:29:41 UTC
244fb97 Refactor `get_tau_sigma` and support lists of variables (#7185) 04 March 2024, 23:16:32 UTC
47f6d9e Fix syntax of some documentation code blocks 04 March 2024, 10:27:38 UTC
f8e24fc Explain how to make the graph from to_graphviz 04 March 2024, 10:27:38 UTC
109dd50 Bump codecov/codecov-action from 3 to 4 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 04 March 2024, 10:25:42 UTC
d95acc0 Updated docstrings in pymc.model.core.Model (#7118) 04 March 2024, 10:24:17 UTC
cb412cb Bump docker/setup-buildx-action from 3.0.0 to 3.1.0 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.0.0 to 3.1.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v3.0.0...v3.1.0) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 04 March 2024, 04:17:04 UTC
46f1675 Add danger warning about buggy behavior of Deterministics in `sample_posterior_predictive` 01 March 2024, 18:21:36 UTC
547e2e0 Add examples for advanced uses of `sample_posterior_predictive` 01 March 2024, 18:21:36 UTC
35ccca5 Fix error in `dataset_to_point_list` when chain, draw are not the leading dims (#7180) 01 March 2024, 14:05:36 UTC
9bf2190 Fix error in warn_treedepth when using multiple NUTS sampler 01 March 2024, 09:50:01 UTC
6c6fd13 Remove sample_posterior_predictive_w, previously deprecated 29 February 2024, 18:57:49 UTC
6252d2e Add gufunc_signature to SymbolicRandomVariables 29 February 2024, 09:06:02 UTC
2f85e66 Remove deprecated Bound distribution 28 February 2024, 11:16:31 UTC
a2988c7 Refactor duplicated jax sampler code and emit convergence warnings by default 28 February 2024, 08:55:33 UTC
bcbb066 Always run divergence and treedepth checks in `run_convergence_checks` 28 February 2024, 08:55:33 UTC
ecbcf38 Rename moment to finite_logp_point (#7166) 28 February 2024, 08:17:21 UTC
d6535e8 Reduce chance to fail for `test_replace_vars_in_graphs_nested_reference` test case (#7174) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 28 February 2024, 08:10:58 UTC
879dc0e Fix typo in developer_guide.md (#7170) 27 February 2024, 09:51:48 UTC
2e3ea56 add sitemap to docs 26 February 2024, 18:05:45 UTC
74748c7 Fix `compute_log_prior` in models with `Deterministics` (#7168) 22 February 2024, 17:15:57 UTC
97a7a00 Reduce number of minimum draw in warning message 20 February 2024, 11:24:01 UTC
7b38a48 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2) 20 February 2024, 09:15:24 UTC
0541065 update BAP to third edition 17 February 2024, 16:03:11 UTC
c3e0d86 Add option to save model graph to an image (#7158) 17 February 2024, 06:33:11 UTC
3a304d6 Remove intX and floatX from distributions (#7114) 17 February 2024, 06:30:33 UTC
0d8ddba Fix copying of shared variables in `fgraph_from_model` (#7153) * Do not use deprecated ScalarSharedVariable * Recreate SharedVariables with exact type in fgraph_from_model 13 February 2024, 18:47:17 UTC
ff99e3b add Google Scholar link for newest article 13 February 2024, 14:18:02 UTC
ae5a943 add log_prior to arviz converter 13 February 2024, 12:24:03 UTC
1eef3d2 update name workflow 13 February 2024, 12:24:03 UTC
726d18b unify 13 February 2024, 12:24:03 UTC
d6297ba add compute_log_prior 13 February 2024, 12:24:03 UTC
6657169 Remove extra line 13 February 2024, 09:14:41 UTC
a9b9e31 Specify automatic labels in dependabot.yml 13 February 2024, 05:18:50 UTC
353af18 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.0...v0.2.1) 13 February 2024, 05:10:20 UTC
dcf1a25 Bump pre-commit/action from 3.0.0 to 3.0.1 Bumps [pre-commit/action](https://github.com/pre-commit/action) from 3.0.0 to 3.0.1. - [Release notes](https://github.com/pre-commit/action/releases) - [Commits](https://github.com/pre-commit/action/compare/v3.0.0...v3.0.1) --- updated-dependencies: - dependency-name: pre-commit/action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> 13 February 2024, 05:08:43 UTC
627a8dd Deprecate `block_diag` from math module in favor of PyTensor (#7132) 08 February 2024, 14:11:21 UTC
8745974 Fix failing VI test due to pytest change (#7144) 08 February 2024, 09:28:54 UTC
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