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

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8eb4284 lint 11 December 2023, 17:26:14 UTC
759c00e Update tests/sampling/test_jax.py Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 11 December 2023, 17:26:14 UTC
b02e045 revert breaking change to have the default behaviour 11 December 2023, 17:26:14 UTC
aa552fc fix tests 11 December 2023, 17:26:14 UTC
07fac5e refactor jax internals to support more kwargs to numpyro 11 December 2023, 17:26:14 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
17bfab2 Bump docker/setup-buildx-action from 2.10.0 to 3.0.0 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.10.0 to 3.0.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v2.10.0...v3.0.0) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 07:22:28 UTC
e0d2f26 Bump docker/metadata-action from 4 to 5 Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 4 to 5. - [Release notes](https://github.com/docker/metadata-action/releases) - [Upgrade guide](https://github.com/docker/metadata-action/blob/master/UPGRADE.md) - [Commits](https://github.com/docker/metadata-action/compare/v4...96383f45573cb7f253c731d3b3ab81c87ef81934) --- updated-dependencies: - dependency-name: docker/metadata-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 07:22:16 UTC
40ffb9a Bump docker/build-push-action from 4.2.1 to 5.0.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.2.1 to 5.0.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/0a97817b6ade9f46837855d676c4cca3a2471fc9...0565240e2d4ab88bba5387d719585280857ece09) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 18 September 2023, 07:22:02 UTC
9227827 Add helper to convert model coords and dims into format accepted by InferenceData 14 September 2023, 10:00:52 UTC
f77372c Bump Pytensor dependency 14 September 2023, 07:25:11 UTC
ec64d40 Do not predefine custom Cholesky and SolveTriangular Ops Also standardize pytensor linalg calls 14 September 2023, 07:25:11 UTC
5a9c8cd Remove unused MvNormalLogp Op 14 September 2023, 07:25:11 UTC
eb7c3b6 Use set_subtensor instead of inc_subtensor in Ordered transform 13 September 2023, 13:13:34 UTC
73dee50 Handle multivariate transforms of univariate distributions correctly Details: * Fix broadcasting bug in univariate Ordered and SumTo1 transform logp, and add explicitly check when building the graph * Raise if univariate transform is applied to multivariate distribution * Checks and logp reduction are applied even when jacobian is not used 13 September 2023, 13:13:34 UTC
d659848 Fix wrong ZeroSumNormal logp expression 12 September 2023, 20:25:22 UTC
881ef46 ⬆️ UPGRADE: Autoupdate pre-commit config (#6901) 12 September 2023, 15:28:34 UTC
fafe89a Bump docker/build-push-action from 4.1.1 to 4.2.1 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.1 to 4.2.1. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/2eb1c1961a95fc15694676618e422e8ba1d63825...0a97817b6ade9f46837855d676c4cca3a2471fc9) --- 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> 11 September 2023, 08:35:58 UTC
2149d17 Bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [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/v3...3df4ab11eba7bda6032a0b82a6bb43b11571feac) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 11 September 2023, 08:35:14 UTC
39a2975 Derive logprob for exp2, log2, log10, log1p, expm1, log1mexp, log1pexp (softplus), and sigmoid transformations (#6826) 07 September 2023, 14:00:33 UTC
f338f10 Update README with current DBDA repo and link 05 September 2023, 14:38:02 UTC
5df5b26 Bump docker/setup-buildx-action from 2.9.1 to 2.10.0 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.9.1 to 2.10.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v2.9.1...v2.10.0) --- 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> 05 September 2023, 14:37:42 UTC
5bba69a Cast `ZeroSumNormal` shape operations to `config.floatX` (#6889) 05 September 2023, 14:36:49 UTC
e6e0fed Deny broadcasting of the measurable input 05 September 2023, 14:00:29 UTC
6d2a289 Logprob derivation for Min of continuous IID variables (#6846) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 04 September 2023, 15:43:23 UTC
f249f12 Graduate fgraph functionality from pymc-experimental 04 September 2023, 09:39:35 UTC
dfb05b6 Remove experimental warning from external nuts samplers. (#6887) 01 September 2023, 10:44:48 UTC
0069e5f Bump PyTensor dependency 30 August 2023, 06:59:20 UTC
ddd1d4b Add `Model.to_graphviz` shortcut (#6865) * add methods * add test structure * fix docstrings * remove networkx method * imptove tests * rename method name * add mock test * Update tests/test_model.py Co-authored-by: Michael Osthege <michael.osthege@outlook.com> * update docsting Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> --------- Co-authored-by: Michael Osthege <michael.osthege@outlook.com> Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 27 August 2023, 22:27:13 UTC
6691943 Add ICAR to the list of distributions in the docs (#6867) 24 August 2023, 11:22:41 UTC
0434f2b ⬆️ UPGRADE: Autoupdate pre-commit config (#6870) Co-authored-by: pymc-bot <pymc-devs@users.noreply.github.com> 24 August 2023, 11:18:45 UTC
9ee5d84 add ICARRV and ICAR (#6831) * add ICARRV and ICAR * reorganized API so W is required, added tests on logp,rng,checks * adjusted tests and api * add ICAR to lists in distributions/__init__.py * fix check_pymc_params_match_rv_op test * deleted unnecessary pytest.mark.parametize * fix check for square matrix + check_pymc_match_rv_op * fix moment test * removed asserts, added tests on sizes * Implementing Bill's comments * add _supp_shape_from_params() 18 August 2023, 16:31:02 UTC
470d474 added instructions for nutpie 16 August 2023, 21:34:02 UTC
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