This project is mirrored from https://github.com/pymc-devs/pymc3.git.
Pull mirroring updated .
- 10 Jun, 2020 1 commit
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Adrian Seyboldt authored
* Allow specification of dims instead of shape * Add pm.TidyData * Create coords for pm.Data(ndarray) * empty commit to trigger CI * Apply suggestions from code review Co-authored-by:
Alexandre ANDORRA <andorra.alexandre@gmail.com> * apply black formatting * address review comments & formatting * Add demonstration of named coordinates/dims * don't require dim names to be identifiers * sort imports * raise ShapeError instead of ValueError * formatting * robustify Dtype and ShapeError * Removed TidyData and refined dims and coords implementation * Changed name of kwarg export_dims and improved docstrings * Add link to ArviZ in docstrings * Removed TidyData from __all__ * Polished Data container NB * Fixed line break in data.py * Fix inference of coords for dataframes * Refined Data container NB * Updated getting started NB with new dims and coords features * Reran getting started NB * Blackified NBs * rerun with ArviZ branch * use np.shape to be compatible with tuples/lists * add tests for named coordinate handling * Extended tests for data container Co-authored-by:
Michael Osthege <m.osthege@fz-juelich.de> Co-authored-by:
Michael Osthege <michael.osthege@outlook.com> Co-authored-by:
Alexandre ANDORRA <andorra.alexandre@gmail.com>
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- 09 Jun, 2020 4 commits
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Michael Osthege authored
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Michael Osthege authored
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Osvaldo Martin authored
* Expand ABC features. * valueerror * update notebook * remove unused import update release notes * fix notebook style and change order params argument
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Michael Osthege authored
* run some tests with arviz master * change the job definition syntax * rename binder job
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- 04 Jun, 2020 1 commit
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Dan Foreman-Mackey authored
* fixing #3939 * fixing introduced bug in fulladapt quadpot
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- 29 May, 2020 1 commit
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Ravin Kumar authored
* Remove unused communication methods * Update GOVERNANCE.md Co-authored-by:
Thomas Wiecki <thomas.wiecki@gmail.com> Co-authored-by:
Thomas Wiecki <thomas.wiecki@gmail.com>
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- 28 May, 2020 1 commit
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Michael Osthege authored
* mention arviz functions by name in warning * convert to InferenceData already in sample function + convert to InferenceData and save metadata to it already in sample() + pass idata instead of trace to convergence check, to avoid duplicate work + directly use arviz diagnostics instead of pymc3 aliases * fix refactoring bugs * fix indentation * add return_inferencedata option + set to None + defaults to False * Fix numpy docstring format. Replaced "<varname>: <type>" with "<varname> : <type>" per numpy guidelines. Fix spelling typo. * pass model to from_pymc3 because of deprecation warning * add test for return_inferencedata option * advise against keeping warmup draws in a MultiTrace * mention #3911 * pin to arviz 0.8.0 and address review feedback * rerun/update notebook to show inferencedata trace * fix typo * make all from_pymc3 accessible to the user * remove duplicate entry, and wording * address review feedback * update arviz to 0.8.1 because of bugfix * incorporate review feedback + more direct use of ArviZ + some wording things * use arviz plot_ppc * also ignore Visual Studio cache * fix warmup saving logic and test * require latest ArviZ patch * change warning to nuget users towards InferenceData * update ArviZ minimum version * address review feedback * start showing the FutureWarning about return_inferencedata in minor release >=3.10 * require arviz>=0.8.3 for latest bugfix Co-authored-by:
rpgoldman <rpgoldman@goldman-tribe.org>
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- 25 May, 2020 1 commit
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Osvaldo Martin authored
* add n_draws and t_sampling report to smc * add _n_tune * update release notes * resolve conflicts
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- 23 May, 2020 1 commit
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Oriol Abril authored
* get docs for stats and plots to link to ArviZ * update release notes
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- 20 May, 2020 1 commit
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Luciano Paz authored
* Drop support for float128 outside of linux and mac * Improve release notes
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- 18 May, 2020 1 commit
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Alexandre ANDORRA authored
* Initial changes to allow pymc3.Data() to support both int and float input data (previously all input data was coerced to float) WIP for #3813 * added exception for invalid dtype input to pandas_to_array * Refined implementation * Finished dtype conversion handling * Added SharedVariable option to getattr_value * Added dtype handling to set_data function * Added tests for pm.Data used for index variables * Added tests for using pm.data as RV input * Ran Black on data tests files * Added release note * Updated release notes * Updated code in light of Luciano's comments * Fixed implementation of integer checking * Simplified implementation of type checking * Corrected implementation for other uses of pandas_to_array Co-authored-by:
hottwaj <jonathan.a.clarke@gmail.com>
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- 15 May, 2020 1 commit
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Luciano Paz authored
* TST: Added test for the failing sampler * BUG: Make Beta.random to use the clipped random number generator * DOC: Added to release notes * Fix the PR link in the release notes * FIX: use scipy.stats and change ref_rand to point to clipped_beta_rvs * FIX: Use np.maximum and np.minimum to work with scalars and arrays
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- 13 May, 2020 1 commit
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Thomas Wiecki authored
* Fix ODE NB. * Rerun ODE NB.
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- 12 May, 2020 2 commits
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Tirth Patel authored
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Tirth Patel authored
* omit examples and tests in coverage * tests are already omited
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- 11 May, 2020 2 commits
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Alexandre ANDORRA authored
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Alexandre ANDORRA authored
* Set start method to forkserver for MacOS * Polished up changes * Added release note
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- 10 May, 2020 1 commit
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Michael Osthege authored
* fix & specify type and shapes for plot_gp_dist * warn user about nan samples closes #3917 * test that UserWarning is triggered when some samples are nan
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- 05 May, 2020 1 commit
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Ahan M R authored
* Closes #3051 - logp numpy array input- fixed Converts 'int' type to <TensorType(int64,Scalar)> to parse value to `astype` and allows arguments to `logp(self,value)` when called with numpy array. * Closes #3051 - Allows numpy array input to logp Allows `logp(self,value)` to take `value` input of type numpy array without errors * fixes #3051 * Fixes #3051 * updated RELEASE-NOTES.md Added the deprecation of `sd` with `sigma` in newer version with DeprecationWarning on usage of `sd`. * directly use floatX * mention #3836 * move all deprecations into their own chapter, as done in previous releases * add regression test Co-authored-by:
Michael Osthege <michael.osthege@outlook.com>
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- 04 May, 2020 1 commit
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Jonathan Sedar authored
* updated the Hogg notebook * attempted to clarify the kwargs in sample() docstring describing how to pass kwargs to the steppers I believe this fixes https://github.com/pymc-devs/pymc3/issues/3197 I also noted this need for more clarity in my updated notebook in this PR `pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb` * Remove deprecated stuff (#3906) * remove file which is not used * remove deprecated code * repair tests and notebooks that used deprecated API * mention #3906 Co-authored-by:
Michael Osthege <zufallsprinzip@hotmail.de> * add deprecation warnings for old backends (#3902) * add deprecation warnings for old backends * mention backend deprecation #3902 * fix typo Co-authored-by:
Colin <ColCarroll@users.noreply.github.com> Co-authored-by:
Michael Osthege <zufallsprinzip@hotmail.de> Co-authored-by:
Colin <ColCarroll@users.noreply.github.com> * minor formatting to notebook and rework of docstring for sample function notebook: dropped all headings one level lower to comply with TOC logic, and very minor language edits sampling.py: clarifired language around single vs compoundstep * updated the Hogg notebook * attempted to clarify the kwargs in sample() docstring describing how to pass kwargs to the steppers I believe this fixes https://github.com/pymc-devs/pymc3/issues/3197 I also noted this need for more clarity in my updated notebook in this PR `pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb` * minor formatting to notebook and rework of docstring for sample function notebook: dropped all headings one level lower to comply with TOC logic, and very minor language edits sampling.py: clarifired language around single vs compoundstep * updates folowing AlexAndorra review: upgrade to arviz=0.7 set prior params to slightly simpler (more justifiable) values, and testvals to simplier defaults explanatory clarifications formatting, typos, * removed the note re step_kwargs, since this PR updates the appropriate docstring * a cell had become markdown, silly. reset it to code and rerun * minor code reformatting via black_nbconvert, final check and re-run * rerun notebook purely as a lazy but safe way to trigger new CI
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- 03 May, 2020 2 commits
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michaelosthege authored
* add deprecation warnings for old backends * mention backend deprecation #3902 * fix typo Co-authored-by:
Colin <ColCarroll@users.noreply.github.com> Co-authored-by:
Michael Osthege <zufallsprinzip@hotmail.de> Co-authored-by:
Colin <ColCarroll@users.noreply.github.com>
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michaelosthege authored
* remove file which is not used * remove deprecated code * repair tests and notebooks that used deprecated API * mention #3906 Co-authored-by:
Michael Osthege <zufallsprinzip@hotmail.de>
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- 01 May, 2020 1 commit
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Brandon T. Willard authored
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- 29 Apr, 2020 1 commit
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Thomas Wiecki authored
* Move logging import as well as set_compiler_flags up. They seem to otherwise not be picked up on newer python versions. * Add Python 3.8 qualifier. * Remove white-space.
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- 28 Apr, 2020 3 commits
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michaelosthege authored
most configurations for pytest-cov must be done via a .coveragerc config file Co-authored-by:
Michael Osthege <zufallsprinzip@hotmail.de>
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Colin authored
* Add jitter+full_adapt initialization * Add tests and benchmarks * Actually save file
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Alexandre ANDORRA authored
* Defined wrapper function on top of LKJCholeskyCov class * Added possibility of changing stds and rho names * Reorganized docs for LKJCholeskyCov * Updated examples for MvNormal * Integrated Adrian's comments * Added release note * Replaced name_stds and name_rho args by postfix * Modified docstring accordingly * Started updated LKJ notebook * Finished updating LKJ NB * Finished updating Radon example NB * Ran Black on NBs
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- 27 Apr, 2020 1 commit
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Thomas Wiecki authored
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- 25 Apr, 2020 1 commit
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Tirth Patel authored
* add matern 1/2 exmaple in notebook * add equation of matern 1/2 kernel in the example
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- 23 Apr, 2020 2 commits
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Michael Osthege authored
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- 21 Apr, 2020 2 commits
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Michael Osthege authored
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Michael Osthege authored
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- 20 Apr, 2020 4 commits
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michaelosthege authored
Import warnings module in timeseries.py.
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Thomas Wiecki authored
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Oriol (ZBook) authored
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Oriol (ZBook) authored
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- 19 Apr, 2020 2 commits
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Michael Osthege authored
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Chris Fonnesbeck authored
minor change in documentation: support of sum is union of supports.
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