Fix pm.DensityDist bug and incorporate latest upstream changes #42
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* update gp-latent nb to use arviz * rerun, run black * rerun after fixes from comments * rerun black
* rewrite radon notebook using ArviZ and xarray Roughly half notebook has been updated * add comments on xarray usage * rewrite 2n half of notebook * minor fix * rerun notebook and minor changes * rerun notebook on pymc3.9.2 and ArviZ 0.9.0 * remove unused import * add change to release notes
…ostics (pymc-devs#3981) * first attempt to vectorize smc kernel * add ess, remove multiprocessing * run multiple chains * remove unused imports * add more info to report * minor fix * test log * fix type_num error * remove unused imports update BF notebook * update notebook with diagnostics * update notebooks * update notebook * update notebook
* Honor discard_tuned_samples during KeyboardInterrupt * Do not compute convergence checks without samples
* Add time values as sampler stats for NUTS * Use float time counters for nuts stats * Add timing sampler stats to release notes * Improve doc of time related sampler stats Co-authored-by: Alexandre ANDORRA <andorra.alexandre@gmail.com> Co-authored-by: Alexandre ANDORRA <andorra.alexandre@gmail.com>
* Drop support for py3.6 * Update RELEASE-NOTES.md Co-authored-by: Colin <ColCarroll@users.noreply.github.com> Co-authored-by: Colin <ColCarroll@users.noreply.github.com>
* Add more info to divergence warnings * Add dataclasses as requirement for py3.6 * Fix tests for extra divergence info * Remove py3.6 requirements
This reverts commit 1bf867e.
Co-authored-by: Adrian Seyboldt <aseyboldt@users.noreply.github.com>
* Merge close remote connection * Manually pickle step method in multiprocess sampling * Fix tests for extra divergence info * Add test for remote process crash * Better formatting in test_parallel_sampling Co-authored-by: Junpeng Lao <junpenglao@gmail.com> * Use mp_ctx forkserver on MacOS * Add test for pickle with dill Co-authored-by: Junpeng Lao <junpenglao@gmail.com>
* Fix posterior pred. sampling keep_size w/ arviz input. Previously posterior predictive sampling functions did not properly handle the `keep_size` keyword argument when getting an xarray Dataset as parameter. Also extended these functions to accept InferenceData object as input. * Reformatting. * Check type errors. Make errors consistent across sample_posterior_predictive and fast_sample_posterior_predictive, and add 2 tests. * Add changelog entry. Co-authored-by: Robert P. Goldman <rpgoldman@sift.net>
* update notebook * move dist functions out of simulator class * fix docstring * add warning and test for automatic selection of sort sum_stat when using wassertein and energy distances * update release notes * fix typo * add sim_data test * update and add tests * update and add tests
…-devs#3989) * fix the expression of periodic kernel * revert change and add doc * FIXUP: add suggested doc string * FIXUP: revertchanges in .gitignore
* Fix for issue 4022. Check for support for `warn` argument in `matplotlib.use()` call. Drop it if it causes an error. * Alternative fix.
… in MLDA notebooks and script examples. This is done because of the bug described in arviz-devs/arviz#1279. The commit also changes a few parameters in the MLDA .py example to match the ones in the equivalent notebook.
* Remove Dirichlet distribution type restrictions Closes pymc-devs#3999. * Add missing Dirichlet shape parameters to tests * Remove Dirichlet positive concentration parameter constructor tests This test can't be performed in the constructor if we're allowing Theano-type distribution parameters. * Add a hack to statically infer Dirichlet argument shapes Co-authored-by: Brandon T. Willard <brandonwillard@users.noreply.github.com>
to keep mlda_develop updated with recent changes.
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Closes #40