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Remove deprecated stuff #3906

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merged 4 commits into from
May 3, 2020

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michaelosthege
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@michaelosthege michaelosthege commented May 2, 2020

This PR removes code that had deprecation warnings since at least version 3.8.

  • breaking changes: For everybody who took deprecation warnings for real, there's no breaking change.
  • docstrings are fine - we'll see how the tests do on Travis
  • without re-running notebooks, removed functions were renamed directly in the source
  • right before it's ready to merge, mention the PR in the RELEASE-NOTES.md

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👍 👍

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codecov bot commented May 2, 2020

Codecov Report

Merging #3906 into master will increase coverage by 0.02%.
The diff coverage is 66.66%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3906      +/-   ##
==========================================
+ Coverage   83.41%   83.43%   +0.02%     
==========================================
  Files         103      103              
  Lines       14190    14165      -25     
==========================================
- Hits        11836    11819      -17     
+ Misses       2354     2346       -8     
Impacted Files Coverage Δ
pymc3/examples/samplers_mvnormal.py 0.00% <0.00%> (ø)
pymc3/sampling.py 86.19% <ø> (+0.71%) ⬆️
pymc3/stats/__init__.py 92.00% <ø> (-1.94%) ⬇️
pymc3/tests/sampler_fixtures.py 96.74% <100.00%> (ø)

@twiecki twiecki merged commit d59a6e8 into pymc-devs:master May 3, 2020
@michaelosthege michaelosthege deleted the remove-deprecated-stuff branch May 3, 2020 10:12
AlexAndorra pushed a commit that referenced this pull request May 4, 2020
* updated the Hogg notebook

* attempted to clarify the kwargs in sample() docstring describing how to pass kwargs to the steppers

I believe this fixes #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 #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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3 participants