GitLab

* 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>

* Expand ABC features.

* valueerror

* update notebook

* remove unused import update release notes

* fix notebook style and change order params argument

* run some tests with arviz master

* change the job definition syntax

* rename binder job

* fixing #3939

* fixing introduced bug in fulladapt quadpot

* 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>

* 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>

* add n_draws and t_sampling report to smc

* add _n_tune

* update release notes

* resolve conflicts

* get docs for stats and plots to link to ArviZ

* update release notes

* Drop support for float128 outside of linux and mac

* Improve release notes

* 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>

* 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

* Fix ODE NB.

* Rerun ODE NB.

* omit examples and tests in coverage

* tests are already omited

* Set start method to forkserver for MacOS

* Polished up changes

* Added release note

* 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.