This project is mirrored from https://github.com/pymc-devs/pymc3.git. Pull mirroring updated .
  1. 09 Jun, 2020 4 commits
  2. 04 Jun, 2020 1 commit
  3. 29 May, 2020 1 commit
  4. 28 May, 2020 1 commit
    • Michael Osthege's avatar
      return_inferencedata option for pm.sample (#3911) · aafa00bc
      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: default avatarrpgoldman <rpgoldman@goldman-tribe.org>
      aafa00bc
  5. 25 May, 2020 1 commit
  6. 23 May, 2020 1 commit
  7. 20 May, 2020 1 commit
  8. 18 May, 2020 1 commit
    • Alexandre ANDORRA's avatar
      Expand pm.Data capacities (#3925) · 1ed04784
      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: default avatarhottwaj <jonathan.a.clarke@gmail.com>
      1ed04784
  9. 15 May, 2020 1 commit
    • Luciano Paz's avatar
      Cap the values that Beta.random can generate. (#3924) · 7f307b91
      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
      7f307b91
  10. 13 May, 2020 1 commit
  11. 12 May, 2020 2 commits
  12. 11 May, 2020 2 commits
  13. 10 May, 2020 1 commit
  14. 05 May, 2020 1 commit
    • Ahan M R's avatar
      Closes #3051 - logp numpy array input fixed (#3836) · 18f1e513
      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: default avatarMichael Osthege <michael.osthege@outlook.com>
      18f1e513
  15. 04 May, 2020 1 commit
    • Jonathan Sedar's avatar
      Update robust glm notebook (#3908) · 727b88ad
      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: default avatarMichael 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: default avatarColin <ColCarroll@users.noreply.github.com>
      Co-authored-by: default avatarMichael Osthege <zufallsprinzip@hotmail.de>
      Co-authored-by: default avatarColin <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
      727b88ad
  16. 03 May, 2020 2 commits
  17. 01 May, 2020 1 commit
  18. 29 Apr, 2020 1 commit
  19. 28 Apr, 2020 3 commits
  20. 27 Apr, 2020 1 commit
  21. 25 Apr, 2020 1 commit
  22. 23 Apr, 2020 2 commits
  23. 21 Apr, 2020 2 commits
  24. 20 Apr, 2020 4 commits
  25. 19 Apr, 2020 2 commits
  26. 18 Apr, 2020 1 commit