https://github.com/pymc-devs/pymc3

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9ab8afa ⬆️ UPGRADE: Autoupdate pre-commit config 05 February 2024, 07:02:35 UTC
075d304 Merge remote-tracking branch 'origin/main' into create-pr-action/pre-commit-config-update-0 05 February 2024, 07:02:22 UTC
94020c9 Move 'Implementing a Random Variable' to last position in 'How To' section 29 January 2024, 17:45:18 UTC
f8b19a5 Fix RUF005 27 January 2024, 15:06:10 UTC
4140361 Fix RUF013 27 January 2024, 15:06:10 UTC
ba56b81 Fix RUF015 27 January 2024, 15:06:10 UTC
07a14f2 Remove useless str in fstring 27 January 2024, 15:06:10 UTC
86279f8 Enable RUF lints 27 January 2024, 15:06:10 UTC
2ee5813 Upgrade ruff to Python 3.9 27 January 2024, 15:06:10 UTC
2da4050 Allow jitter boolean to be set through nuts_sampler_kwargs (#7083) 23 January 2024, 14:11:26 UTC
ef1f91f Add a flag to LKJCorr to return the unpacked correlation matrix (#7100) * LKJCorr now has an option of returning n by n matrix instead of just the upper triangular part as vector 23 January 2024, 14:10:43 UTC
08eaeb1 [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.14) 23 January 2024, 03:25:05 UTC
f7e51ec ⬆️ UPGRADE: Autoupdate pre-commit config 22 January 2024, 07:02:35 UTC
90392a6 Merge remote-tracking branch 'origin/main' into create-pr-action/pre-commit-config-update-0 22 January 2024, 07:02:22 UTC
d6951a6 Bump actions/cache from 3 to 4 Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 22 January 2024, 05:28:17 UTC
e3f008a Fix progress bar for parallel sampling 21 January 2024, 03:09:18 UTC
3a59c16 update links to Welcome bot images 16 January 2024, 09:58:49 UTC
01757e1 Gitpod instructions: use latest version of pymc (#7106) Co-authored-by: Ben Mares <services-git-throwaway1@tensorial.com> 15 January 2024, 16:35:20 UTC
df4fe5f ⬆️ UPGRADE: Autoupdate pre-commit config 15 January 2024, 07:02:22 UTC
6f8f9ee Extend `dataset_to_point_dict` to accept both dataset and dict of dataarray (#7097) 12 January 2024, 18:45:36 UTC
2051d0b Use ruff linter (#7091) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> Co-authored-by: Ben Mares <services-git-throwaway1@tensorial.com> 11 January 2024, 14:09:24 UTC
2c355f1 suppressed pip install bambi output in GLM core notebook 08 January 2024, 14:34:50 UTC
4e80b37 Bump docker/metadata-action from 5.3.0 to 5.5.0 Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 5.3.0 to 5.5.0. - [Release notes](https://github.com/docker/metadata-action/releases) - [Commits](https://github.com/docker/metadata-action/compare/31cebacef4805868f9ce9a0cb03ee36c32df2ac4...dbef88086f6cef02e264edb7dbf63250c17cef6c) --- updated-dependencies: - dependency-name: docker/metadata-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 08 January 2024, 07:15:15 UTC
7bb2ccd ⬆️ UPGRADE: Autoupdate pre-commit config and update copyright year (#6915) 02 January 2024, 10:43:49 UTC
118be0f Add test for Blockwise logp regression 21 December 2023, 11:15:13 UTC
986738f added normal logcdf func and new test domains 21 December 2023, 11:14:37 UTC
72534c7 Constant fold original RV.shape in graph of joined PartialObservedRV Not doing this would lead to no default updates for draws of such RVs, due to the same RNG being reused twice. 21 December 2023, 11:11:24 UTC
904a0ea Bump docker/metadata-action from 5.0.0 to 5.3.0 Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 5.0.0 to 5.3.0. - [Release notes](https://github.com/docker/metadata-action/releases) - [Commits](https://github.com/docker/metadata-action/compare/96383f45573cb7f253c731d3b3ab81c87ef81934...31cebacef4805868f9ce9a0cb03ee36c32df2ac4) --- updated-dependencies: - dependency-name: docker/metadata-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 13 December 2023, 14:01:03 UTC
011b78b Bump actions/setup-python from 4 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 13 December 2023, 14:00:29 UTC
851c991 Fix default transform for `LKJCorr` (#7065) 13 December 2023, 13:58:47 UTC
35cd657 Allow batched scalar sigma in ZeroSumNormal 13 December 2023, 12:38:25 UTC
0fd7b9e Update PULL_REQUEST_TEMPLATE.md 11 December 2023, 21:31:54 UTC
2e05854 Avoid inplace mutation in replace_rvs_by_values This would happen when transforms reference other variables 10 December 2023, 11:35:08 UTC
01ddcb8 HSGP periodic (#6877) * implement periodic psd and pass test * simplify hsgp test, set up for mark other cov_func * attempt at if-else logic in HSGP class API * np.pi in w0 * check arguments for period and nonperiod case * tests run but failing * fix one of the mypy errors * periodic cov pytest uses J not m because mpyp * avoid AttributeError by init parameterization * get rid of mypy "None" error * self.prior_linearized inside if avoids double call * need to add the mean function in prior * run pre-commit locally * add docs to test about why test_prior fails * freshen up the docs * improve coverage of args * mypy ignore type * fix parameterization test * use power_spectral_density_approx because cant sum * tbe -> the typo docs * expand warning and change the triggering clause * separate into HSGP and HSGPPeriodic * remove commented periodic in HSGP test * appease mypy * add scale parameter for HSGP 10 December 2023, 05:34:27 UTC
a1dce17 Use dataset.sizes instead of dataset.dims A FutureWarning is issued in 'xarray==2023.12.0' 09 December 2023, 20:59:22 UTC
4de076d Improve PR template (#7052) 09 December 2023, 17:00:43 UTC
02cbac6 Update installation instructions to remove incompatibility of JAX on Windows 29 November 2023, 13:18:22 UTC
005ba5f Another small fixes in docs and imports (#7030) * Remove old import from autosummary doc pages * Fix small error * Correct place for model_to_networkx & model_to_graphviz * Correct currentmodule source for pytensorf.rst * Update docs/source/api/model/core.rst Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> * Fix sampling & jax docs imports --------- Co-authored-by: Denis Kataev <denis.a.kataev+git@gmail.com> Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> 29 November 2023, 00:58:47 UTC
915e6a2 Better float32 sampling support for TruncatedNormal (#7026) * manually inv transform; force rng same type * always upcast f64 and downcast to dtype of param * add comment * use class attr dtype * need else stmt for dtype * actually no need to downcast in this method * rm unused import 28 November 2023, 13:15:45 UTC
f8b142a Bump Pytensor dependency to >=2.18.1,<2.19 25 November 2023, 07:44:12 UTC
0b85d02 Deprecate pytensor_config 24 November 2023, 15:35:56 UTC
bbfd69e Deprecate Model.model property 24 November 2023, 15:35:56 UTC
43ddea3 Remove deprecated model methods 24 November 2023, 15:35:56 UTC
2fb312b Update GOVERNANCE.md (#7031) * Update GOVERNANCE.md * Update GOVERNANCE.md Co-authored-by: Purna Chandra Mansingh <purnachandramansingh135@gmail.com> --------- Co-authored-by: Purna Chandra Mansingh <purnachandramansingh135@gmail.com> 24 November 2023, 02:36:40 UTC
8ec1f08 Use PyTensor StudentT RV 23 November 2023, 22:33:52 UTC
ec70d86 Fix docs formatting in `shape_utils` (#7025) * Small docs update shape_utils.py Fix docs markup * Update to_tuple docs shape_utils.py * Types --------- Co-authored-by: Denis Kataev <denis.a.kataev+git@gmail.com> 23 November 2023, 15:17:16 UTC
373274a update theme (#7018) * update theme version * update conf.py 23 November 2023, 13:03:16 UTC
547bcb4 Deprecate unused function walk_model 18 November 2023, 05:42:46 UTC
cb02b26 Merge functionality of pytensorf and logprob/utils Also fixes circular imports 18 November 2023, 05:42:46 UTC
55cc5aa Remove deprecated function rvs_to_value_vars 18 November 2023, 05:42:46 UTC
25fa5a2 Move ZeroSumTransform methods inside respective class 18 November 2023, 05:42:46 UTC
1b0433f Remove duplicate ChainTransform 18 November 2023, 05:42:46 UTC
04a03b5 Rename RVTransform to Transform 18 November 2023, 05:42:46 UTC
1d7c957 Update devcontainer (#7017) * Update dev container on release and schedule * Use latest version of upstream dev container image * Remove pre-commit cache hack * Add Jupyter extension to container 17 November 2023, 23:08:20 UTC
305eb39 ChiSquared now returns a Gamma random variable (#7007) 17 November 2023, 11:22:51 UTC
cac99d9 Update CODE_OF_CONDUCT.md Changed contact email 14 November 2023, 16:39:39 UTC
ad450a6 Default `moment` for `CustomDist` provided with a `dist` function (#6873) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 13 November 2023, 15:16:56 UTC
d7415de Fix typo in distribution dimensionality (#7005) The order of shape got probably mixed-up here. 10 November 2023, 12:31:07 UTC
ec24ce6 Change random_seed in test_car_rng_fn 08 November 2023, 12:58:03 UTC
693dd34 Allow IntervalTransform to handle dynamic infinite bounds Fixes bug in partially observed truncated variable 08 November 2023, 12:58:03 UTC
6b051f9 Disable progressbar in SMC tests on Windows 08 November 2023, 11:31:00 UTC
5360939 Do not create new Ops in TransformValuesRewrite 08 November 2023, 11:31:00 UTC
33a6af1 Move value transform logic to its own logprob file 08 November 2023, 11:31:00 UTC
ec4407d Recognize alternative form of sigmoid in logprob inference 03 November 2023, 12:15:07 UTC
714b4a0 Fix compute_test_value error when creating observed variables (#6982) Co-authored-by: Ricardo Vieira <ricardo.vieira1994@gmail.com> 02 November 2023, 10:11:26 UTC
58217cc Add more missing functions to math module 01 November 2023, 12:52:09 UTC
419af06 Support logp derivation of `power(base, rv)` (#6962) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> Co-authored-by: Luke LB <ll17354@bristol.ac.uk> 26 October 2023, 05:24:39 UTC
c53277b Run pre-commit and mypy on oldest supported Python version (#6969) * Run pre-commit and mypy on oldest supported Python version * Fix type hints invalid with Python 3.9 25 October 2023, 13:00:11 UTC
6b486b9 Fix truncated rejection sampling for scalar RVs 24 October 2023, 14:25:49 UTC
efa0d34 Logprob derivation of Max for Discrete IID distributions (#6790) 24 October 2023, 13:23:37 UTC
c3f93ba Improve blackjax sampling integration (#6963) * More fine tune control in blackjax sampling. * Formatting * FIx test * Enable progress bar for sampling * use standard processbar kwarg 23 October 2023, 13:20:25 UTC
009da35 Bump actions/checkout from 4.1.0 to 4.1.1 Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.0 to 4.1.1. - [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/8ade135a41bc03ea155e62e844d188df1ea18608...b4ffde65f46336ab88eb53be808477a3936bae11) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> 23 October 2023, 10:32:00 UTC
e0c9c64 Swap expand_dims of Periodic and WrappedPeriodic kernel full method 22 October 2023, 13:01:21 UTC
5f29b25 switching fill and fill_like to full and full_like 20 October 2023, 11:24:25 UTC
3dddaf5 Adding functions to math.py issue #6948 20 October 2023, 11:24:25 UTC
eb1d63a Use numpy testing utilities instead of custom close_to* (#6961) * Use np.testing asserts in test_transform.py * Fix test_simplex_accuracy - The previous identity_f function returned an empty array. This was missed by our check but captured by numpy. * Replace custom close_to function in tests/helpers.py * Replace custom close_to function in test_dist_math.py * Replace custom close_to function in tuning/test_starting.py * Remove reduntant file tests/checks.py * Use absolute tolerance in check_transform 20 October 2023, 10:31:14 UTC
03f9f72 Fix HurdleLogNormal Docstring (#6958) Correct the psi parameter description so that it refers to the correct distribution for this class. Co-authored-by: amcadie <amcadie@ebay.com> 17 October 2023, 16:01:10 UTC
a772a79 Add expression for NegativeBinomial variance Co-authored-by: lucianopaz <luciano.paz.neuro@gmail.com> 17 October 2023, 12:20:18 UTC
827918b Improve multinomial moment (#6933) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 14 October 2023, 15:04:40 UTC
cb64480 Add constant and observed data to nutpie idata (#6943) * Add constant and observed data to nutpie idata * change order and add comment to revert 12 October 2023, 14:20:03 UTC
6f4a040 Make Model.str_repr robust to variables without monkey-patch 11 October 2023, 15:26:12 UTC
df7b267 Install jax things from a separate environment file 11 October 2023, 13:28:08 UTC
57d73cc Fix type hints Python 3.9 compatibility 11 October 2023, 13:28:08 UTC
3bc68bf Fix typing in `model.transform.basic` 11 October 2023, 13:28:08 UTC
059ce45 Return `VarName` type from `get_var_name` function 11 October 2023, 13:28:08 UTC
41f0181 Fix typing in `opvi` and `model_graph` 11 October 2023, 13:28:08 UTC
07adbc8 Fix mypy errors 11 October 2023, 13:28:08 UTC
9e6818b Bump mypy to 1.5.1 11 October 2023, 13:28:08 UTC
602234b Default zero mu for MvNormal and MvStudentT 04 October 2023, 16:14:09 UTC
ce543da Allow batched parameters in MvNormal and MvStudentT distributions 04 October 2023, 16:14:09 UTC
a3ec9a5 Fix mypy failure 02 October 2023, 14:27:42 UTC
55e8fe9 Add regression test for Truncated Gamma 02 October 2023, 14:27:42 UTC
f2bf1e0 Update PyTensor dependency 02 October 2023, 14:27:42 UTC
7c0a095 Fix do/conditioning model docs (#6936) 02 October 2023, 08:39:31 UTC
5ed39c3 Re-execute notebook 29 September 2023, 10:24:54 UTC
e7965fd Bump actions/checkout from 4.0.0 to 4.1.0 Bumps [actions/checkout](https://github.com/actions/checkout) from 4.0.0 to 4.1.0. - [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/3df4ab11eba7bda6032a0b82a6bb43b11571feac...8ade135a41bc03ea155e62e844d188df1ea18608) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> 25 September 2023, 20:27:29 UTC
15fbf0e Fix jax sampling (#6922) 25 September 2023, 06:48:43 UTC
54269df Update pymc_overview.ipynb (#6925) * Update pymc_overview.ipynb Fix typo in overview notebook * Update pymc_overview.ipynb 24 September 2023, 11:15:39 UTC
bc4b51d Fix fgraph_from_model with multivariate transformed variables (#6924) * fix do with transformed * Change test --------- Co-authored-by: Ricardo Vieira <ricardo.vieira1994@gmail.com> 23 September 2023, 00:14:03 UTC
a24acb9 Bump docker/login-action from 2 to 3 Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/v2...343f7c4344506bcbf9b4de18042ae17996df046d) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 07:22:41 UTC
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