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

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4e6527c Bump version to 4.0.0 🎉 03 June 2022, 15:51:31 UTC
e663f46 Remove developer guide. Needs to be updated eventually. 03 June 2022, 15:50:44 UTC
938604c Add temporary fix for pretty representation of SymbolicDistributions 03 June 2022, 15:13:01 UTC
57c6a8f Move printing-related tests to their own test module 03 June 2022, 15:13:01 UTC
c758d0d Restructure Release Notes (#5832) * 1st try at restructuring * Add emojis and do-not-miss section * Apply suggestions from code review Co-authored-by: Michael Osthege <michael.osthege@outlook.com> Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> * Improve structure based on review * Apply suggestions from code review Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> * Improve structure again * Add release announcement * Apply suggestions from code review Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> * Apply suggestions from code review Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> * Apply suggestions from code review Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> * Add highlight of JAX backend. * Remove BART section and move links to where we remove it. * Move BART further down. Remove mention of size. Co-authored-by: Michael Osthege <michael.osthege@outlook.com> Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> 03 June 2022, 14:43:38 UTC
0d38abf Move BMCP to top of book list 03 June 2022, 14:28:34 UTC
5da32ed Add comment to `set_data` condition where the length comes from a `shape[i]` graph 03 June 2022, 14:28:09 UTC
70b0c49 Automatically resize independently mutable dims via `set_data` 03 June 2022, 14:28:09 UTC
2120593 Warn about resizing `MutableData` dims that are not symbolically linked Closes #5812 03 June 2022, 14:28:09 UTC
a74592a Add `Model.set_dim` method for safer dims resizing 03 June 2022, 14:28:09 UTC
0e7cd1f Update guide on implementing new distributions Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> 03 June 2022, 13:38:09 UTC
2dc0009 Add troubleshooting tips on pre-commit 03 June 2022, 13:38:09 UTC
48eff60 Write instructions on running the test suite 03 June 2022, 13:38:09 UTC
559969c Update Aesara dependency 02 June 2022, 22:37:35 UTC
2d6304d fix 404 and intersphinx 02 June 2022, 22:33:32 UTC
88a0f43 Bring back learn page. (#5833) * Bring back learning page. * Remove no-sidebar. * Updates to user guide. * Remove learn.md. * Add link to PyMC Labs. * Link to correct image. * Improve cosulting page. Rename to learn. * Change cards to use Oriol's proposed format. * fix sphinx build * add newline at end of file * ensure img kwarg is in the next line of directive definition Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> 02 June 2022, 19:39:29 UTC
de9db67 Deprecate remaining VI methods (#5806) * Deprecated remaining VI methods * Deleted flows and code for local and batched kwarg * removed rowwise from opvi.py * redo the test_variational_inference.py * refactored some test cases * removed mention of local from docstring * refactor some test in varialional_inference * did correction in docstring * removed batched dimension property * added symbolic_random * removed part = 'total' * refactor test_logq_globals and test_pickle_approx test * refactor test_init_groups 02 June 2022, 16:05:04 UTC
b073fd8 Remove user-facing mentions of size in timeseries distributions 02 June 2022, 16:02:50 UTC
343a6f5 Use more wide default init_dist in GaussianRandomWalk and AR and raise UserWarning when not explicitly defined 02 June 2022, 16:02:50 UTC
12039e0 Rename GaussianRandomWalk `init` argument to `init_dist` and fix some type hints 02 June 2022, 16:02:50 UTC
42e3745 Do not issue warning when default transform of Mixture is None Also fixes typo in warning message 02 June 2022, 14:22:05 UTC
db5c87e Update navbar (#5830) * start updating navbar * get navbar and redirects to work * make search bar return the same results from all websites * update requirements * remove search bar from sidebar * fix urls and add extra page * Update .pre-commit-config.yaml Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> 01 June 2022, 10:38:10 UTC
1e7d91f Make Metropolis cope better with multiple dimensions Metropolis now updates each dimension sequentially and tunes a proposal scale parameter per dimension 31 May 2022, 21:20:17 UTC
4810829 Move TestMetropolisProposal tests to TestMetropolis 31 May 2022, 21:20:17 UTC
6750ea7 Supress warning SMC initialization (#5827) 31 May 2022, 17:23:07 UTC
6027be1 Raise NotImplementedError in sample_posterior_predictive_w 31 May 2022, 16:26:29 UTC
ae578c2 Raise NotImplementedError in not yet refactored timeseries distributions Co-authored-by: Thomas Wiecki <thomas.wiecki@gmail.com> 31 May 2022, 16:26:29 UTC
5703a9d Remove advanced Aesara usage guide (#5826) 30 May 2022, 18:03:08 UTC
6b22ed5 Add return type hints (#5819) * Add return type hints * Add type hints for rv arguments * Fix more type issues Closes #4880 Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 30 May 2022, 17:44:55 UTC
57654dc Add name to CompountStep 30 May 2022, 16:28:55 UTC
35393af Avoid unnecessary slow compilation of Aesara functions in test_step 30 May 2022, 16:28:55 UTC
e636852 Refactor TestStepMethods and reduce number of draws The number of draws was set too high to accommodate the worst / buggy samplers (see #5815) 30 May 2022, 16:28:55 UTC
70a3e0b Refactor Slice.astep method Avoid recreation of RaveledArrays in inner loops and repeated indexing of `self.w` 30 May 2022, 16:28:55 UTC
f28f9cf Fix Slice sampler bugs introduced in b988ba99a084a18b2c907ef2ee4aeb1f4ab56160 1. The previous interval was of the form `[q0 - uniform(0, self.w), q0 + self.w]` which is not symmetric around q0 in expectation, breaking detailed balance. 2. The left/right bound values used for updating earlier variables were only set to the accepted values during tuning. This might have made bug 1 worse. 30 May 2022, 16:28:55 UTC
de55543 Add Quick links to Contributing guidelines (#5818) 30 May 2022, 09:54:42 UTC
4d2f3a8 Fallback to Aeppl when logp is not implemented 26 May 2022, 12:24:49 UTC
7d7d07c Update Aeppl dependency 26 May 2022, 12:24:49 UTC
7b239bb Limit model graph nodes to named model variables Some nodes such as `NoneConst` in an Aesara graph are named, but aren't model variables that the user is interested in. 26 May 2022, 11:06:24 UTC
2161664 Forward `dims` to reparametrized `Deterministic` This way `.prior(..., dims=...)` applies not only to the `_rotated_` RV but also to the `Deterministic` that the user is interested in. 26 May 2022, 10:26:41 UTC
9ca57bf Fix shape problem in GP priors Shape asserts were added in existing tests that covered both reparameterize=True/False. Closes #5803 26 May 2022, 10:26:41 UTC
b67a76f Pin blackjax version for testing to fix failing CI Related to https://github.com/blackjax-devs/blackjax/issues/212 26 May 2022, 10:26:41 UTC
2adb346 Fix ReleaseNotes 25 May 2022, 04:41:03 UTC
62e1e9d Seed sampling in TestNutsCheckTrace.test_linalg 24 May 2022, 20:33:39 UTC
15431d9 Fix non-deterministic NUTS initialization when using ADVI 24 May 2022, 20:33:39 UTC
cee2b30 Remove model.rng_seeder and allow compile_pymc to reseed RNG variables in compiled function Sampling functions now also accept RandomState or Generators as input to random_seed, similarly to how random_state behaves in scipy distributions. For backwards compatibility this argument was not renamed. 24 May 2022, 20:33:39 UTC
09240fc Update expected behavior of `sample`-related tests in relation to global seeding. Together, `test_sample_does_not_set_seed` and `test_parallel_sample_does_not_reuse_seed` covered two unspoken behaviors of `sample`: 1. When no seed is specified, PyMC shall not set global seed state of numpy in the main process. 2. When no seed is specified, sampling will depend on numpy global seeding state for reproducible behavior. Point 1 is due to PyMC legacy dependency on global seeding for step samplers. It tries to minimize "damage" by only setting global seeds when it absolutely needs to, in order to ensure deterministic sampling. Ideally calls to `numpy.seed` would never be made. Point 2 goes against NumPy current best practices of using None when defining new Generators / SeedSequences (https://numpy.org/doc/stable/reference/random/bit_generators/generated/numpy.random.SeedSequence.html#numpy.random.SeedSequence) The refactored tests cover point 1 more directly, and assert the opposite of point 2. 24 May 2022, 20:33:39 UTC
c71fd4e Fix default use of global seeding 24 May 2022, 20:33:39 UTC
4caa5b9 Refactor RandomState/Generator reseeding logic in initial_point into aesaraf 24 May 2022, 20:33:39 UTC
b5a5b56 Remove size from Distribution signatures (#5788) * Remove size from .dist() signature Closes #5754 * Align (Half)Flat signatures with superclass * Don't mention size in the docstring Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> * Revert changes in `rng_fn` signatures Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> 23 May 2022, 13:49:41 UTC
d0af6b1 New `var_names` kwarg for `pm.model_to_graphviz` (#5634) Enables positive selection of model variables to be included in the model graph. Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 22 May 2022, 11:23:21 UTC
66fba38 Add warning about unobserved continuous censored distributions Co-authored-by: Michael Osthege <michael.osthege@outlook.com> Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 22 May 2022, 07:47:33 UTC
a95dd71 Require `pm.MutableData` or `add_coord(mutable=True)` for mutable dims This increases the safety of working with resizable dimensions. Dims created via `pm.Model(coords=...)` coordinates are now immutable. Only dimension lengths that are created anew from `pm.MutableData`, `pm.Data(mutable=True)`, or the underlying `add_coord(mutable=True)` will become shared variables. Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 21 May 2022, 19:47:02 UTC
7ec106c Optionally pass `coords` when creating `pm.Data` variables Needed to create resizable dims with coordinate values, because coords passed to the model will become immutable dims. See https://github.com/pymc-devs/pymc/pull/5763. Also, because `pm.Data` variables can be N-dimensional, the coordinate values can't reliably be taken from the value. 21 May 2022, 19:47:02 UTC
e83520e Remove ShapeWarning in favor of raising ValueError directly 21 May 2022, 19:47:02 UTC
2b7a3c2 add calendar to website (#5786) * add calendar to website * update navbar about item to pymc.io * update urls in intersphinx mapping * add description above the calendar 20 May 2022, 15:16:31 UTC
b91283e Pass seed to `find_map` and set global seeds in `_iter_sample` and `_prepare_iter_sample` This reverts some changes in 47b61def5f24830e36714886356557a0e3918195 which wrongly disabled global seeding in some sampling contexts that still depended on it. 19 May 2022, 22:05:24 UTC
56ad6a9 Add explanation to test_sample_does_not_set_seed 19 May 2022, 22:05:24 UTC
f0c8f55 Update pr_tutorial.md (#5724) * Update pr_tutorial.md Make the python version consistent on the PR tutorial. * update to python 3.9 19 May 2022, 22:03:57 UTC
00d4372 Update distribution-related changes in RELEASE-NOTES.md 19 May 2022, 05:48:12 UTC
c2d96cf Use unit normal as default init_dist in GaussianRandomWalk and AR 19 May 2022, 05:48:12 UTC
2536920 add subsections inside community section (#5782) 19 May 2022, 04:03:35 UTC
82f70fc Filter deterministics from initial_points returned by init_nuts 18 May 2022, 09:35:43 UTC
817f457 Remove size parameter from sample_posterior_predictive 18 May 2022, 08:05:20 UTC
862bd05 Add compile_forward_sampling_function 17 May 2022, 16:55:36 UTC
4969460 Move Identity operator initialization close to class definition 17 May 2022, 14:40:33 UTC
c327a02 Remove take_along_axis in favor of Aesara's implementation 17 May 2022, 14:40:33 UTC
8520a2c Make test_sample_posterior_predictive_after_set_data_with_coords more robust Closes #5739 17 May 2022, 13:13:39 UTC
85468b0 Improve errors and warnings related to dimension resizing (#5761) * Support TensorConstant entries in `Model.dim_lengths`. * Raise errors on attempts to resize dims with `TensorConstant` length. * Raise errors on attempts to resize dims that are linked to non-shared variables. * Warn about resizing dims that weren't initialized from a shared variable (supposedly via `add_coord(..., fixed=False)`, see #5763). * Raise errors when attempting to resize a dim that had coord values without providing new coord values. Closes #5760 by anticipating that not all symbolic dim lengths originate from RVs. Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 16 May 2022, 17:41:48 UTC
3b4da05 doc: add `nuts_kwargs` to `sample_numpyro_nuts` docstring (#5764) The `nuts_kwargs` argument is currently missing from the docstring of `sample_numpyro_nuts`. This just adds a simple statement to indicate that the keyword arguments are passed to `numpyro.infer.NUTS()`. 15 May 2022, 04:14:38 UTC
ab593b1 Remove `EllipticalSlice` sampler Closes #5137 09 May 2022, 19:58:08 UTC
ce2e891 Update doc links in README (#5753) * Update links to overview and examples. * Overview links fixed. 09 May 2022, 11:23:41 UTC
e7bfc25 ⬆️ UPGRADE: Autoupdate pre-commit config 09 May 2022, 11:23:06 UTC
49eecfb Introduced tests for pymc.distributions.logprob._get_scaling_ (#5544) * Introduced test for _get_scaling_ Co-authored-by: Icyshaman <vikasvishwakarma6787@gmail.com> Co-authored-by: chritter <christian.ritter@canada.ca> 08 May 2022, 12:42:12 UTC
53ad689 Refactor get_tau_sigma to handle lists (#5747) * Refactor get_tau_sigma to handle lists * Fixed syntax error * Black formatted * Change assertions to ValueError raises * Prior predictions constant data (#5723) * support return constant_data with prior pred * pre-commit format * added test * code review * Fix issue probably-meant-fstring found at https://codereview.doctor (#5726) * Add coords argument to pymc.set_data (#5588) Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com> * remove MultinomialRV override * ⬆️ UPGRADE: Autoupdate pre-commit config * Group GaussianRandomWalk tests in single class * Infer steps from shape in GaussianRandomWalk * Unpin upper limit on numpydoc Closes #5401 * ⬆️ UPGRADE: Autoupdate pre-commit config * Standardize docstrings of input dists arguments and add warning about cloning * Remove unnecessary tag in Simulator logp * Replace deprecated tag.ignore_logprob * Group compile_pymc tests in own class * Remove remaining uses of default_updates in codebase * Remove redundant/wrong docstrings from GaussianRandomWalk logp * Add moment to GaussianRandomWalk and fix mu/sigma broadcasting bug * Do not create temporary SymbolicDistribution just to retrieve number of RNGs needed Reordered methods for consistency * Move SymbolicDistribution docstring to body of class * Refactor AR distribution * Deprecates AR1 distribution * Implements random and moment methods * Batching works on the left as with other distributions * Rename `pandas_to_array` to `convert_observed_data` * Obtain step information from dims and observed * Make AR steps extend shape beyond initial_dist This is consistent with the meaning of steps in the GaussianRandomWalk and translates directly to the number of scan steps taken Co-authored-by: TimOliverMaier <tmaier01@students.uni-mainz.de> Co-authored-by: code-review-doctor <72647856+code-review-doctor@users.noreply.github.com> Co-authored-by: Somasree Majumder <56045049+soma2000-lang@users.noreply.github.com> Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com> Co-authored-by: danhphan <danh.phan.mq@gmail.com> Co-authored-by: twiecki <twiecki@users.noreply.github.com> Co-authored-by: Ricardo <ricardo.vieira1994@gmail.com> Co-authored-by: Ravin Kumar <ravinsdrive@gmail.com> Co-authored-by: Michael Osthege <michael.osthege@outlook.com> 06 May 2022, 17:30:44 UTC
dd23c90 Make AR steps extend shape beyond initial_dist This is consistent with the meaning of steps in the GaussianRandomWalk and translates directly to the number of scan steps taken 06 May 2022, 11:37:19 UTC
812a52c Obtain step information from dims and observed 06 May 2022, 11:37:19 UTC
9a905fa Rename `pandas_to_array` to `convert_observed_data` 06 May 2022, 11:37:19 UTC
c76b9b9 Refactor AR distribution * Deprecates AR1 distribution * Implements random and moment methods * Batching works on the left as with other distributions 05 May 2022, 08:02:42 UTC
c18e6ce Move SymbolicDistribution docstring to body of class 05 May 2022, 08:02:42 UTC
4471204 Do not create temporary SymbolicDistribution just to retrieve number of RNGs needed Reordered methods for consistency 05 May 2022, 08:02:42 UTC
21c2e6c Add moment to GaussianRandomWalk and fix mu/sigma broadcasting bug 04 May 2022, 14:49:45 UTC
1a5b3d6 Remove redundant/wrong docstrings from GaussianRandomWalk logp 04 May 2022, 14:49:45 UTC
a3bd083 Remove remaining uses of default_updates in codebase 04 May 2022, 11:54:11 UTC
ee73231 Group compile_pymc tests in own class 04 May 2022, 11:54:11 UTC
138a64f Replace deprecated tag.ignore_logprob 04 May 2022, 11:54:11 UTC
b05af43 Remove unnecessary tag in Simulator logp 04 May 2022, 11:54:11 UTC
f95e839 Standardize docstrings of input dists arguments and add warning about cloning 04 May 2022, 11:54:11 UTC
4ae8b07 ⬆️ UPGRADE: Autoupdate pre-commit config 03 May 2022, 22:13:58 UTC
5c39f7e Unpin upper limit on numpydoc Closes #5401 01 May 2022, 09:33:45 UTC
6ae7628 Infer steps from shape in GaussianRandomWalk 29 April 2022, 15:30:08 UTC
c80657e Group GaussianRandomWalk tests in single class 29 April 2022, 15:30:08 UTC
54425cd ⬆️ UPGRADE: Autoupdate pre-commit config 27 April 2022, 16:44:31 UTC
458f28e remove MultinomialRV override 27 April 2022, 12:52:44 UTC
bae5087 Add coords argument to pymc.set_data (#5588) Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com> 24 April 2022, 08:46:27 UTC
e4ec363 Fix issue probably-meant-fstring found at https://codereview.doctor (#5726) 24 April 2022, 02:13:20 UTC
162ad6c Prior predictions constant data (#5723) * support return constant_data with prior pred * pre-commit format * added test * code review 22 April 2022, 21:16:03 UTC
d322f75 Upgrade Aesara and Aeppl dependencies 20 April 2022, 11:48:16 UTC
bc0ec61 Remove unnecessary at.squeeze in logp and logcdf of Mixtures 20 April 2022, 11:48:16 UTC
d60b4cf Correct xfail reason in test_nested_mixture 20 April 2022, 11:48:16 UTC
d02707e Move GaussianRandomWalk init resizing to Op.make_node 19 April 2022, 19:33:23 UTC
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