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21 April 2024, 10:16:19 UTC
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c22ea96 Maxim Kochurov 30 March 2022, 09:44:36 UTC Scope separator for netcdf (#5663) * add a failing test * fix a failing test with changes in model.py * better test * change docs in model.py * fix tests * use :: saparator * fix typo 30 March 2022, 09:44:36 UTC
ab93967 Ricardo 30 March 2022, 06:00:43 UTC Bump version for b6 release 30 March 2022, 09:25:46 UTC
b536f91 Ricardo 30 March 2022, 05:51:39 UTC Remove stale `test_sample_generate_values` sample_posterior_predictive no longer accepts non-integer samples 30 March 2022, 07:36:59 UTC
7aafe10 Ricardo 30 March 2022, 05:49:16 UTC Update stale xfail tests 30 March 2022, 07:36:59 UTC
042a1c5 Ricardo 30 March 2022, 05:43:01 UTC Add rng update test for size from observed 30 March 2022, 07:36:59 UTC
5392468 Ricardo 29 March 2022, 09:30:30 UTC Update "traditional" rng default_update in `change_rv_size` A "traditional" update is `rng.default_update = rv_constructor(rng=rng).owner.outputs[0]` 29 March 2022, 18:35:56 UTC
b9cdd5c Ricardo 29 March 2022, 09:19:32 UTC Rename internal variables in `change_rv_size` 29 March 2022, 18:35:56 UTC
72f255d Ricardo 29 March 2022, 09:07:54 UTC Do not set default_updates in RandomVariables returned by PyMC distributions 29 March 2022, 18:35:56 UTC
4984ef3 Ricardo 29 March 2022, 10:43:09 UTC Do not set rng updates for RandomVariables that are not computed in the graph 29 March 2022, 18:35:56 UTC
73c9e3c Rob Zinkov 29 March 2022, 11:30:49 UTC Recognize cast data in InferenceData 29 March 2022, 11:30:49 UTC
fa015e3 Ricardo 21 March 2022, 11:44:29 UTC Implement default transform for Mixtures 28 March 2022, 09:18:27 UTC
0b9f9cb Ricardo 21 March 2022, 12:25:35 UTC Specify `default_output` of MarginalMixtureRV This is necessary for transforms to work with Aeppl 28 March 2022, 09:18:27 UTC
21b289a Ricardo 21 March 2022, 10:15:56 UTC Use dispatching for default transform instead of overriding `__new__` 28 March 2022, 09:18:27 UTC
f0cdb1f Ricardo 21 March 2022, 10:25:56 UTC Pass rv to `_default_transform` dispatch function 28 March 2022, 09:18:27 UTC
324d900 Ricardo 21 March 2022, 10:07:18 UTC Rename `_get_default_transform` to `_default_transform` 28 March 2022, 09:18:27 UTC
d8f7d22 Ricardo 22 March 2022, 08:44:18 UTC Rename `moment_marginal_mixture` function For consistency with other Mixture dispatched functions 28 March 2022, 09:18:27 UTC
623fc91 Ricardo 21 March 2022, 10:06:07 UTC Rename `get_moment` to `moment` 28 March 2022, 09:18:27 UTC
9c2ba7a Thomas J. Fan 25 March 2022, 19:59:26 UTC Remove pandas dependency (#5633) * CLN Removes pandas import from tests * FIX Adds importorskip to test_data_container * MAINT Removes pandas dependency 25 March 2022, 19:59:26 UTC
7aa520c Ricardo 23 March 2022, 11:59:31 UTC Add test for interactions between missing, default and explicit updates in `compile_pymc` 25 March 2022, 16:49:44 UTC
e4a07c1 Michael Osthege 24 March 2022, 11:17:06 UTC Upgrade all cache actions to v3 24 March 2022, 13:54:00 UTC
d322b81 Ricardo 22 March 2022, 09:01:35 UTC Refine Interval docstrings and fix typo 23 March 2022, 12:19:23 UTC
0246701 twiecki 21 March 2022, 07:04:35 UTC ⬆️ UPGRADE: Autoupdate pre-commit config 22 March 2022, 16:30:59 UTC
40937a7 Purna Chandra Mansingh 22 March 2022, 10:53:09 UTC Update docstring of SkewNormal, Triangular, Gumbel, Logistic, LogitNormal (#5596) * fixed doctring of SkewNormal * fixed doctring of Triangular * fixed doctring of pymc.Gumbel * fixed doctring of pymc.Logistic * fixed doctring of pymc.LogitNormal * fixed optional parameters 22 March 2022, 10:53:09 UTC
c20cda2 Purna Chandra Mansingh 22 March 2022, 10:51:57 UTC Update docstring in Interpolated, Rice, Moyal, AsymmetricLaplace and PolyaGamma distribution (#5600) 22 March 2022, 10:51:57 UTC
ff694fb Purna Chandra Mansingh 22 March 2022, 10:47:43 UTC Update docstring in ChiSquared, HalfNormal, Wald, Pareto, ExGaussion and VonMiese distribution (#5595) * Fixed ChiSquared, HalfNormal, Wald, Pareto, ExGaussion and VonMiese docstring * fixed optional parameter * fixed TensorVariable 22 March 2022, 10:47:43 UTC
a281885 Ricardo 22 March 2022, 08:53:01 UTC Bump version for b5 release 22 March 2022, 09:50:41 UTC
7a6bd02 Michael Osthege 20 March 2022, 14:54:29 UTC Ignore flaky sampling_jax.py mypy results 21 March 2022, 20:55:10 UTC
80b5e86 Michael Osthege 20 March 2022, 14:26:32 UTC Upgrade dependencies in pre-commit environment 21 March 2022, 20:55:10 UTC
4e21ae5 Michael Osthege 20 March 2022, 14:16:30 UTC Remove `BaseStochasticGradient` step method Closes #5138 21 March 2022, 20:55:10 UTC
52682eb Purna Chandra Mansingh 21 March 2022, 20:40:32 UTC Parametrize Binomial and Categorical distributions via logit_p (#5637) 21 March 2022, 20:40:32 UTC
5b31ec7 Osvaldo Martin 21 March 2022, 19:24:30 UTC Fix bug with default init_nuts (#5622) 21 March 2022, 19:24:30 UTC
436f94a Michael Osthege 20 March 2022, 15:05:59 UTC Parametrize some more tests by floatX 21 March 2022, 16:36:04 UTC
0fb7999 Michael Osthege 20 March 2022, 13:44:21 UTC Run only selected tests under float32 Closes #5626 21 March 2022, 16:36:04 UTC
e2cfd11 Michael Osthege 20 March 2022, 13:25:52 UTC Remove XFAILed exact sample comparison test 21 March 2022, 16:36:04 UTC
e77e238 Ricardo 18 March 2022, 13:46:55 UTC Raise ValueError if random variables are present in the logp graph Aeppl allows for graphs containing random variables. PyMC models do not generally allow for this, with the current exception of models that include SimulatorRVs. 21 March 2022, 11:48:28 UTC
b895e40 Michael Osthege 20 March 2022, 00:46:39 UTC Fix Windows jobs & redistribute to reduce runtime Closes #5475 20 March 2022, 11:31:41 UTC
e0a0325 Michael Osthege 19 March 2022, 17:28:28 UTC Drop latest ArviZ tests, upgrade to Ubuntu 20.04 and add MacOS jobs 20 March 2022, 11:31:41 UTC
8087861 Michael Osthege 19 March 2022, 14:40:20 UTC Combine test workflows The steps within each job were not changed in this commit. 20 March 2022, 11:31:41 UTC
0a9e99e Michael Osthege 19 March 2022, 14:56:49 UTC Remove old, unused build script 20 March 2022, 11:31:41 UTC
a8e5b53 Michael Osthege 19 March 2022, 21:21:55 UTC Update contributing guide with etiquette section (#5611) * Update outdated parts of contributing guide and PR template * Add section on contribution etiquette Co-authored-by: Ravin Kumar <ravinsdrive@gmail.com> Co-authored-by: Oriol Abril <oriol.abril.pla@gmail.com> 19 March 2022, 21:21:55 UTC
849a64d Michael Osthege 18 March 2022, 17:29:00 UTC Refine trigger filter for both PRs and pushes Previously only one of the trigger conditions had the filter. This is a follow-up to #5364. 19 March 2022, 14:39:27 UTC
8b063f9 Ricardo 18 March 2022, 14:15:39 UTC Do not set RNG updates inplace in compile_pymc 18 March 2022, 18:44:18 UTC
80f8195 Ricardo 18 March 2022, 11:52:44 UTC Rename `logp_transform` to `_get_default_transform` and move it to transforms.py 18 March 2022, 14:34:16 UTC
02860d3 Ricardo 18 March 2022, 12:40:09 UTC Do not make transforms module accessible at root level 18 March 2022, 14:24:54 UTC
4e8f96b Ricardo 13 January 2022, 12:55:02 UTC Create helper wrapper around Aeppl IntervalTransform 18 March 2022, 14:24:54 UTC
f0f4252 Ricardo 13 January 2022, 12:54:34 UTC Add docstrings to transforms.simplex 18 March 2022, 14:24:54 UTC
144b0ba Maxim Kochurov 18 March 2022, 12:44:52 UTC WIP Improve scoped models (#5607) * use slashes to separate context * add fix for nested prefix * fix test * refactor prefix * revert precommit change * fix windows issue * fis smc test * Update pymc/tests/test_model.py Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> * Update pymc/tests/test_model.py Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> * update tests Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 18 March 2022, 12:44:52 UTC
e8c07ef Purna Chandra Mansingh 18 March 2022, 11:01:53 UTC Remove sd optional kwarg from distributions (#5583) 18 March 2022, 11:01:53 UTC
a0cff37 markvrma 15 February 2022, 15:34:38 UTC Generalize Multinomial moment to arbitrary dimensions 18 March 2022, 10:44:34 UTC
5a44793 Ricardo 18 March 2022, 09:27:20 UTC Make rv_size_is_none more robust 18 March 2022, 10:44:34 UTC
2db28f0 Michael Osthege 17 March 2022, 09:41:30 UTC Bump for b4 release 17 March 2022, 11:19:10 UTC
07f5847 Michael Osthege 16 March 2022, 17:33:02 UTC Repair pip install step in arviz workflow The non-SSL cloning is no longer supported by GitHub. 17 March 2022, 01:02:16 UTC
416d49f S 16 March 2022, 07:42:37 UTC Updated convert_shape and convert_size Closes #5394 17 March 2022, 01:02:16 UTC
09bddde theorashid 15 March 2022, 14:23:05 UTC Allow n=0 in Binomial logp and logcdf 15 March 2022, 14:23:05 UTC
08b6b01 Michael Osthege 12 March 2022, 15:37:14 UTC Fix more typing problems 15 March 2022, 10:14:43 UTC
97f0f79 Michael Osthege 12 March 2022, 15:25:58 UTC Make `joint_logp` always return lists when `sum=False` 15 March 2022, 10:14:43 UTC
7cc570a Ricardo 14 March 2022, 13:28:15 UTC Rename ZeroInflatedPoisson theta parameter to mu For consistency with the base Poisson distribution 14 March 2022, 21:01:07 UTC
e89b594 Ricardo 14 March 2022, 13:23:30 UTC Replace ZeroInflated distributions with Mixtures 14 March 2022, 21:01:07 UTC
7d4006f Ricardo 13 March 2022, 14:49:21 UTC Round moment of discrete mixtures 14 March 2022, 21:01:07 UTC
7ec9a24 Ricardo 11 March 2022, 16:52:50 UTC Allow broadcasting of mixture components 14 March 2022, 21:01:07 UTC
5410885 Ricardo 11 March 2022, 15:43:54 UTC Implement Mixture logcdf 14 March 2022, 21:01:07 UTC
0190aa5 Ricardo 11 March 2022, 17:45:18 UTC Test Mixture dtype 14 March 2022, 21:01:07 UTC
21a2ba1 Ricardo 11 March 2022, 15:54:46 UTC Implement Constant logcdf 14 March 2022, 21:01:07 UTC
edb832c Ricardo 11 March 2022, 17:25:22 UTC Allow Constant to be integer or float 14 March 2022, 21:01:07 UTC
8cb71a5 Rob Zinkov 13 March 2022, 11:56:02 UTC Adding release notes for recent changes to `sampling_jax` This fixes #5587 14 March 2022, 10:00:14 UTC
cf73e9c twiecki 14 March 2022, 07:05:19 UTC ⬆️ UPGRADE: Autoupdate pre-commit config 14 March 2022, 09:00:42 UTC
0a1993f theorashid 13 March 2022, 14:35:45 UTC Use checkout action in nightly workflow (#5591) 13 March 2022, 14:35:45 UTC
86f8d98 Purna Chandra Mansingh 12 March 2022, 08:22:17 UTC Update pymc.HalfStudentT docsting (#5555) * fixed pymc.HalfStudentT docsting * added :context: close-figs and removed sd from dist * undo the sd change 12 March 2022, 08:22:17 UTC
a14e4f9 Purna Chandra Mansingh 12 March 2022, 08:22:08 UTC Update pymc.HalfCauchy docsting (#5554) * fixed pymc.HalfCauchy docsting * added :context: close-figs 12 March 2022, 08:22:08 UTC
7c3900c Purna Chandra Mansingh 12 March 2022, 08:21:59 UTC Update pymc.Cauchy docsting (#5553) * fixed pymc.Cauchy docsting * added :context: close-figs 12 March 2022, 08:21:59 UTC
32380ec Purna Chandra Mansingh 12 March 2022, 08:21:23 UTC Update pymc.StudentT docsting (#5552) * fixed pymc.StudentT docsting * removed sd from dist * undo the sd change 12 March 2022, 08:21:23 UTC
b9d4bb8 Purna Chandra Mansingh 12 March 2022, 08:21:04 UTC Update pymc.Laplace docsting (#5551) * fixed pymc.Laplace docsting * fixed pymc.Laplace docsting 12 March 2022, 08:21:04 UTC
7f434bb Purna Chandra Mansingh 12 March 2022, 08:20:49 UTC Update pymc.TruncatedNormal docstring (#5546) * fixed TruncateNormal docsting * fixed TruncateNormal docsting * removed sd from dist * undo the sd change 12 March 2022, 08:20:49 UTC
54c9dfa Christian Ritter 12 March 2022, 08:20:33 UTC update Exponential numpydoc (#5491) Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> 12 March 2022, 08:20:33 UTC
5eaa516 Ricardo 11 March 2022, 15:24:23 UTC Update aesara and aeppl dependencies 11 March 2022, 20:19:58 UTC
b799547 Rob Zinkov 11 March 2022, 20:18:35 UTC Adding NUTS sampler from blackjax to sampling_jax (#5477) * Adding NUTS sampler from blackjax to sampling_jax * Lint fixes * Refactor get_jaxified_logp * Install blackjax in workflows * Fix url * Simplify function * Add documentation * Add library versions * Move to more appropriate section * Fix docstrings * Add jax to dev environment * Jax doesn't work on windows, remove it * Exclude jax * Fix merge * Remove progress bar functionality for now * Pre-commit fix 11 March 2022, 20:18:35 UTC
65dcb49 Sagar 11 March 2022, 15:26:23 UTC Return an empty string for empty model representation (#5577) 11 March 2022, 15:26:23 UTC
4626712 aloctavodia 10 March 2022, 10:25:03 UTC fix extract_Q_estimate function 11 March 2022, 09:36:53 UTC
b903e57 aloctavodia 10 March 2022, 08:06:39 UTC stack array stats 11 March 2022, 09:36:53 UTC
c3c76c5 Michael Osthege 11 March 2022, 02:23:09 UTC Run mypy in pre-commit for continuous improvement of type hints (#5549) * Remove numpy Tester instance from public API It was making mypy follow into the tests module regardles of its config. See https://stackoverflow.com/a/70367929 * Move all mypy config to mypy.init Because typing_copilot can't deal with the other formats. * Fix typing problems and add pre-commit mypy step 11 March 2022, 02:23:09 UTC
b919153 Osvaldo Martin 10 March 2022, 22:10:43 UTC update release note (#5573) 10 March 2022, 22:10:43 UTC
d150d55 mirko-m 10 March 2022, 19:09:27 UTC Add tests for the output type of ode_func (#5414) Co-authored-by: Mirko Moeller <mirko.moeller@coanda.ca> Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 10 March 2022, 19:09:27 UTC
069de73 Purna Chandra Mansingh 10 March 2022, 18:42:23 UTC Update pymc.LogNormal docsting (#5556) * fixed pymc.LogNormal docsting * fixed pymc.LogNormal docsting 10 March 2022, 18:42:23 UTC
44c5495 theorashid 09 March 2022, 23:03:22 UTC use grep from __init__.py to get version 10 March 2022, 09:13:44 UTC
2dd4c8c aloctavodia 08 March 2022, 15:29:26 UTC allow external step method 10 March 2022, 08:22:09 UTC
50ceb2b aloctavodia 08 March 2022, 09:54:00 UTC remove bart 10 March 2022, 08:22:09 UTC
620b11d Ricardo Vieira 09 March 2022, 02:56:09 UTC Refactor Mixture distribution for V4 (#5438) * Set `expand=True` when calling `change_size` in `SymbolicDistribution` * Move NormalMixture tests to their own class * Move mixture random tests from test_distributions_random to test_mixture * Use specific imports in test_mixture * Reenable Mixture tests in pytest workflow * Refactor Mixture distribution Mixtures now use an `OpFromGraph` that encapsulates the Aesara random method. This is used so that logp can be easily dispatched to the distribution without requiring involved pattern matching. The Mixture random and logp methods now fully respect the support dimensionality of its components, whereas previously only the logp method did, leading to inconsistencies between the two methods. In the case where the weights (or size) indicate the need for more draws than what is given by the component distributions, the latter are resized to ensure there are no repeated draws. This refactoring forces Mixture components to be basic RandomVariables, meaning that nested Mixtures or Mixtures of Symbolic distributions (like Censored) are not currently possible. Co-authored-by: Larry Dong <larry.dong@mail.utoronto.ca> * Add warning when using iterable with single Mixture component * Update Mixture docstrings * Emphasize equivalency between iterable of components and single batched component * Add example with mixture of two distinct distributions * Add example with multivariate components * Refactor NormalMixture * Refactor TestMixtureVsLatent The two tests relied on implicit behavior of V3, where the dimensionality of the weights implied the support dimension of mixture distribution. This, however, led to inconsistent behavior between the random method and the logp, as the latter did not enforce this assumption, and did not distinguish if values were mixed across the implied support dimension. In this refactoring, the support dimensionality of the component variables determines the dimensionality of the mixture distribution, regardless of the weights. This leads to consistent behavior between the random and logp methods as asserted by the new checks. Future work will explore allowing the user to specify an artificial support dimensionality that is higher than the one implied by the component distributions, but this is for now not possible. * Remove MixtureSameFamily Behavior is now implemented in Mixture * Add Mixture moments * Update release notes Co-authored-by: Larry Dong <larry.dong@mail.utoronto.ca> 09 March 2022, 02:56:09 UTC
7d4162c Purna Chandra Mansingh 08 March 2022, 13:54:40 UTC fixed pymc.Kumaraswamy docsting (#5550) 08 March 2022, 13:54:40 UTC
afe210a Chris Fonnesbeck 07 March 2022, 17:43:10 UTC Initiate v4.0.0b3 release (#5562) * Initiate v4.0.0b3 release * Added Maintenance section to release notes with VI update notice * Clean release notes * Removed Cholesky from non-working section of release notes Co-authored-by: Ricardo <ricardo.vieira1994@gmail.com> 07 March 2022, 17:43:10 UTC
f71a2b1 Ricardo 03 March 2022, 10:00:10 UTC Automatically resize `sd_dist` in `_LKJCholeskyCov` 07 March 2022, 16:02:14 UTC
5023a70 aloctavodia 25 February 2022, 08:27:01 UTC fix predictions when using 1 chain 07 March 2022, 15:57:11 UTC
55463de theorashid 07 March 2022, 11:21:52 UTC use new secret for nightly build 07 March 2022, 11:38:37 UTC
a98ab6d Thomas J. Fan 07 March 2022, 06:05:25 UTC CLN Remove pandas from bart.utils.plot_dependence (#5558) 07 March 2022, 06:05:25 UTC
620546b Purna Chandra Mansingh 06 March 2022, 02:39:53 UTC Doc change the default value of pymc.draw from 500 to 1. (#5543) * changed the default value of drwas from 500 to 1 * fixed samplers_draw docsting * fixed samplers_draw docsting 06 March 2022, 02:39:53 UTC
4223b6e Larry Dong 04 March 2022, 01:10:03 UTC replace assert_op by raise_op 04 March 2022, 08:45:51 UTC
6833677 Osvaldo Martin 04 March 2022, 06:45:55 UTC update reported warnings after sampling (#5516) * update report * update per comments 04 March 2022, 06:45:55 UTC
999160a theorashid 03 March 2022, 18:19:50 UTC adding nightly builds (#5490) * this isn't aesara anymore * release-job didn't exist * remove get_versions() * more functions, less faff * nicer f string * NIGHTLY is a global variable * testing nightly install with date in workflow 03 March 2022, 18:19:50 UTC
a0e43da Ricardo 03 March 2022, 13:38:18 UTC Remove pylint skip-file in sampling_jax.py 03 March 2022, 15:14:44 UTC
64e9375 Ricardo 03 March 2022, 13:37:12 UTC Add type hints to several functions in sampling_jax.py 03 March 2022, 15:14:44 UTC
dd4b940 Ricardo 03 March 2022, 13:25:48 UTC Fix seeding bug in `sample_numpyro_nuts` when more than one chain was sampled 03 March 2022, 15:14:44 UTC
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