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

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Revision Author Date Message Commit Date
e597d7d Add Hilbert Space Student T Process 07 November 2023, 15:12:03 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
273375d fix format library citation 16 August 2023, 12:36:08 UTC
67438dd update citation 16 August 2023, 11:40:34 UTC
13a2310 Seed flaky TestHSGP.test_prior 16 August 2023, 10:20:07 UTC
90fd8a3 Add JAX implementation of PosDefMatrix Op 16 August 2023, 10:20:07 UTC
1a3bfd9 Make PosDefMatrix Op output type boolean 16 August 2023, 10:20:07 UTC
3fbe9a9 Remove SpecifyShape from Assert JAX 16 August 2023, 10:20:07 UTC
0d75490 Fix TestMatrixNormal.check_draws Test behavior was accidentally changed in 9dad9c2baeef9d19c7cd7ff740e30843e66df93e 16 August 2023, 10:20:07 UTC
9956991 Fix CDF and iCDF derivations based on monotonicity 13 August 2023, 18:13:46 UTC
15b41f0 Fix probability of cosh transform 13 August 2023, 18:13:46 UTC
745b444 Re-organize test_transforms.py 13 August 2023, 18:13:46 UTC
bb3bda2 Use numpy.testing.assert_allclose in test_transforms.py 13 August 2023, 18:13:46 UTC
accabdf Adding description to Gumbel Distribution (#6810) * adding description to Gumbel Distribution" * Apply suggestions from code review Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> * Adding fix for the suggestions * "to" -> "of" --------- Co-authored-by: larryshamalama <larry.dong@mail.utoronto.ca> 13 August 2023, 15:34:00 UTC
a4b0581 Add colors to tests 12 August 2023, 13:40:31 UTC
a2695a7 Bump docker/build-push-action from 4.0.0 to 4.1.1 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.0.0 to 4.1.1. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/3b5e8027fcad23fda98b2e3ac259d8d67585f671...2eb1c1961a95fc15694676618e422e8ba1d63825) --- 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> 10 August 2023, 08:42:29 UTC
d59a960 Do not include seeded_test fixture in exported BaseTestDistributionRandom 08 August 2023, 12:11:18 UTC
ccad4c8 Use `ordered_univariate` in documentation example of NormalMixture (#6842) 06 August 2023, 15:37:16 UTC
2644f2c Bump docker/setup-buildx-action from 2.4.1 to 2.9.1 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.4.1 to 2.9.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v2.4.1...v2.9.1) --- 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 August 2023, 07:21:24 UTC
65cf4c2 ⬆️ UPGRADE: Autoupdate pre-commit config 03 August 2023, 16:14:24 UTC
06bf9df remove SeededTest class 02 August 2023, 13:10:02 UTC
50d056d Assert warmup/posterior lengths in `StepMethodTesteer` 02 August 2023, 10:07:48 UTC
55079d1 Fix regression #6840 The `tune` attribute is reset by the sampling iterator. Closes #6840 02 August 2023, 10:07:48 UTC
5c600c7 Use graph_replace instead of clone_replace in VI 31 July 2023, 08:34:05 UTC
1a06d50 Raise NotImplementedError for multivariate CustomDists 31 July 2023, 08:34:05 UTC
2303bf9 Bump PyTensor dependency to 2.14.1 31 July 2023, 08:34:05 UTC
f9e6418 Make test_inference tests fail on unexpected warnings 31 July 2023, 08:34:05 UTC
e3961fc Logprob derivation for Max (#6769) 27 July 2023, 07:58:48 UTC
510d3b8 Restrict domain on alpha in the CAR distribution (#6801) * Restricted alpha to be greater than -1 and less than 1. Adjusted parameter checks. * Ricardo's suggestions * add tests for code-cov * logp test, test rename, np.all - > np.any 26 July 2023, 20:06:26 UTC
cd1d354 Mark object stats as `str`-typed 24 July 2023, 15:06:57 UTC
65eb592 Fix duplicate `"tune"` stat in McBackend adapter 24 July 2023, 15:06:57 UTC
38e87e2 Emit `"tune"` from all stepmethods 24 July 2023, 15:06:57 UTC
63483b7 ⬆️ UPGRADE: Autoupdate pre-commit config (#6784) * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config * ⬆️ UPGRADE: Autoupdate pre-commit config --------- Co-authored-by: pymc-bot <pymc-devs@users.noreply.github.com> 22 July 2023, 21:57:22 UTC
82c6318 Add GP Wrapped Periodic Kernel (#6742) Co-authored-by: Joseph Hall <joseph.hall@bp.com> 19 July 2023, 15:52:50 UTC
4a65148 GP Covariance Function Type Hints (#6740) Co-authored-by: Joseph Hall <joseph.hall@bp.com> 19 July 2023, 12:44:30 UTC
42f2e91 Drop support for Python 3.8 18 July 2023, 19:09:00 UTC
2269d73 Don't use size and simplify dims example in dimensionality notebook 17 July 2023, 10:10:28 UTC
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