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* 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

* 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>

* 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

* 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>

* 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>

* 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.

most configurations for pytest-cov must be done via a .coveragerc config file
Co-authored-by: Michael Osthege <zufallsprinzip@hotmail.de>

* Add jitter+full_adapt initialization

* Add tests and benchmarks

* Actually save file

* 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

* add matern 1/2 exmaple in notebook

* add equation of matern 1/2 kernel in the example

Import warnings module in timeseries.py.

minor change in documentation: support of sum is union of supports.

Added raw string qualifiers for docstrings that were causing the deprecation warnings in issue #3878.
In passing, fixed some other minor docstring formatting issues.

[MRG] ENH: Fix array wrap in gp submodule to allow one dimensional arrays

* Added Moyal distribution to continuous class. Added tests for Moyal distribution.

* Release notes updated.

* Added float32 exception for Moyal dist in tests.

* move change from V3.8 to V3.9

#3852 adds the new feature to the V3.8 changelog while it should go in the V3.9 changelog.

* fix small typo

* move the change a little down in the changelog

* ENH: add exponentiation with a scalar

* fix the scalar condition

* add examples in notebook

* Added check that a>0 in Dirichlet

* Cast a as array for tests

* Test a>0 only when a not an RV and convert to array when list

* Added test for init of Dirichlet with negative values

* Added release note

* Resolved conflict in release notes

* Escaped parenthesis in match regexp

* Added wrapper for gamma sampling in negative binomial distribution.

* Fixed typo in posterior sampling warnings.

* Drop nuts init method from pm.sample (#3863)

* Dropped nuts init method

* Dropped nuts init method from tests

* Refined doc string and added release note

* Added wrapper for gamma sampling in negative binomial distribution.

* Fixed typo in posterior sampling warnings.

* Added test for negative binomial input shape.

* Updating release notes with changes to negative binomial sampling.
Co-authored-by: Alexandre ANDORRA <andorra.alexandre@gmail.com>

* Dropped nuts init method

* Dropped nuts init method from tests

* Refined doc string and added release note

* Added example plot for the Rice distribution.

* Updated for scipy rice distribution convention.

* Reordering sigmas in rice docstring.

* Changed sampling defaults and cleaned typos

* Switched tune default to 1000

* Added release note

* Moved release note under Maintenance

* Changed sampling defaults and cleaned typos

* Finished updating PPC section

* Finished updating prediction section

* Ran whole NB

* Ran Black

* Revert "Changed sampling defaults and cleaned typos"

This reverts commit 5c08d9289a381cee6b678d385163b3b20185959c.

Revert changes made in sampling file

* Updated posterior pred NB

The layout of parameters sections was wrong.
Also pruned some dead code.

* ls

* Changes to ode.rst to make docs appear.

* Should be working now