Shap

This release contains a number enhancements and bug fixes.

What's Changed

Added
* Faster and more stable linear solver in KernelShap by lorentzenchr in https://github.com/shap/shap/pull/3271
* Enabled passing of `ax` to `group_difference()` plot by mtlulka in https://github.com/shap/shap/pull/3355
* Added support for Explanation.display_data in bar plot by fountaindive in https://github.com/shap/shap/pull/3386
* Improved build messages when building from source by connortann in https://github.com/shap/shap/pull/3403

Fixed
* Fixed `CatboostClassifier` explanations with feature interactions on Windows by CloseChoice in https://github.com/shap/shap/pull/3325
* Fixed passing of Xgboost model parameters to xgboost.DMatrix by vancromy in https://github.com/shap/shap/pull/3314
* Explicit specification of xgboost>=1.4 constraint by mtlulka in https://github.com/shap/shap/pull/3352
* Fixed conversion of DMatrix to CSR matrix by thatlittleboy in https://github.com/shap/shap/pull/3359
* Removed deprecated `use_line_collection` in `dependence_plot` by CloseChoice in https://github.com/shap/shap/pull/3369
* Fixed bug relating to array reshaping in `scatter` plots by SomeUserName1 in https://github.com/shap/shap/pull/2799

Documentation
* A large number of [example notebooks](https://shap.readthedocs.io/en/latest) fixed and updated by connortann, znacer , thatlittleboy, CloseChoice and stompsjo

New Contributors
* vancromy made their first contribution in https://github.com/shap/shap/pull/3314
* lorentzenchr made their first contribution in https://github.com/shap/shap/pull/3271
* mtlulka made their first contribution in https://github.com/shap/shap/pull/3352
* fountaindive made their first contribution in https://github.com/shap/shap/pull/3386
* SomeUserName1 made their first contribution in https://github.com/shap/shap/pull/2799
* stompsjo made their first contribution in https://github.com/shap/shap/pull/3391

**Full Changelog**: https://github.com/shap/shap/compare/v0.43.0...V0.44.0

What's Changed

This release contains a number of bug fixes and improvements.

Following the [NEP 29 deprecation policy](https://numpy.org/neps/nep-0029-deprecation_policy.html), this release drops support for python 3.7.

Breaking changes

* Removed the deprecated Boston dataset by thatlittleboy in https://github.com/shap/shap/pull/3316
* The shape of `Explanation.base_values` has been standardised between different TreeExplainer models to always be of shape `(N,)` and not `(N,1)`. By thatlittleboy in https://github.com/shap/shap/pull/3121

Added
* Added additivity check to Pytorch DeepExplainer (activated by default) by noxthot in https://github.com/shap/shap/pull/3265
* Added flag to allow the printing of the mean SHAP value in the legend of a multi-output bar plot. By 101AlexMartin in https://github.com/shap/shap/pull/3062
* Added heatmap and violin plot to top-level API by connortann in https://github.com/shap/shap/pull/3157
* Replaced all tqdm imports with tqdm.auto by owenlamont in https://github.com/shap/shap/pull/3199

Fixed
* Fixed segmentation faults on MacOS with lightgbm tests (with newer libomp versions) by thatlittleboy in https://github.com/shap/shap/pull/3093
* Support LightGBM ensemble containing single leaf trees (stump) by thatlittleboy in https://github.com/shap/shap/pull/3094
* Fixed conversion DataFrame to ndarray for Explanation.data by danieleongari in https://github.com/shap/shap/pull/3131
* Fixed waterfall plot on explanations of sklearn tree models by connortann in https://github.com/shap/shap/pull/3138
* Fixed pandas input for gradient explainer by Koen-Git in https://github.com/shap/shap/pull/3153
* Fixed slicing of `feature_names` in Explanation objects with square `.values` by thatlittleboy in https://github.com/shap/shap/pull/3126
* Correct xlim in force_matplotlib in cases where the signs of force are all the same by zaburo-ch in https://github.com/shap/shap/pull/2839
* Fixed ngboost explanations when col_sample < 1 by CloseChoice in https://github.com/shap/shap/pull/3294
* Fixed torch additivity check in PyTorch DeepExplainer by noxthot in https://github.com/shap/shap/pull/3281
* Replaced print statements with warnings in DeepExplainer by znacer in https://github.com/shap/shap/pull/3264
* Replace deprecated `register_backward_hook()` by noxthot in https://github.com/shap/shap/pull/3259
* Fixed deprecated use of xgboost early_stopping_rounds by CloseChoice in https://github.com/shap/shap/pull/3306
* Fixed 3rd party deprecation warnings: numba, xgboost, typing, distutils by connortann in https://github.com/shap/shap/pull/3084
* Updated the Javascript bundle to update deprecated dependencies by connortann in https://github.com/shap/shap/pull/2974

There have also been a large number of improvements to the tutorials and examples, by connortann, znacer, arshiaar, thatlittleboy, dsgibbons, owenlamont and CloseChoice

New Contributors
* 101AlexMartin made their first contribution in https://github.com/shap/shap/pull/3062
* znacer made their first contribution in https://github.com/shap/shap/pull/3112
* danieleongari made their first contribution in https://github.com/shap/shap/pull/3131
* Koen-Git made their first contribution in https://github.com/shap/shap/pull/3153
* pre-commit-ci made their first contribution in https://github.com/shap/shap/pull/3173
* owenlamont made their first contribution in https://github.com/shap/shap/pull/3199
* arshiaar made their first contribution in https://github.com/shap/shap/pull/3201
* dsgibbons made their first contribution in https://github.com/shap/shap/pull/3200
* noxthot made their first contribution in https://github.com/shap/shap/pull/3265
* zaburo-ch made their first contribution in https://github.com/shap/shap/pull/2839
* CloseChoice made their first contribution in https://github.com/shap/shap/pull/3282

**Full Changelog**: https://github.com/shap/shap/compare/v0.42.1...v0.43.0

Patch release to provide wheels for a broader range of architectures.

Added

* Added wheels for linux:aarch64 and macos:arm64 by PrimozGodec in https://github.com/slundberg/shap/pull/3078 and connortann in https://github.com/slundberg/shap/pull/3083.

Fixed

* Fixed circular import issues with shap.benchmark by thatlittleboy in https://github.com/slundberg/shap/pull/3076.
* Fixed TestPyPI releases workflow by connortann in https://github.com/slundberg/shap/pull/3068
* Fix further flaky tests by thatlittleboy in https://github.com/slundberg/shap/pull/3073
* Fix shap.summary_plot to work with matplotlib 3.6.0 by jklaise in https://github.com/slundberg/shap/pull/2697
* Fix benchmark top-level import by thatlittleboy in https://github.com/slundberg/shap/pull/3076
* Fix ipython import warning from top-level shap import by connortann in https://github.com/slundberg/shap/pull/3090

**Full Changelog**: https://github.com/slundberg/shap/compare/v0.42.0...v0.42.1

This release incorporates many changes that were originally contributed by the SHAP community via dsgibbons's [Community Fork][fork], which has now been merged into the main shap repository. PRs from this origin are labelled here as `fork123`.

This will be the last release that supports python 3.7.

[fork]: https://github.com/slundberg/shap/discussions/2942

Added

- Added support for python 3.11 ([fork72](https://github.com/dsgibbons/shap/pull/72) by connortann).
- Added `n_points` parameter to all functions in `shap.datasets` ([fork39](https://github.com/dsgibbons/shap/pull/39) by thatlittleboy).
- Added `__call__` to `KernelExplainer` ([2966](https://github.com/slundberg/shap/pull/2966) by dwolfeu).
- Added [contributing guidelines][contrib-guide] ([2996](https://github.com/slundberg/shap/pull/2996) by connortann).

[contrib-guide]: [https://github.com/slundberg/shap/blob/master/CONTRIBUTING.md]

Fixed

- Fixed `plot.waterfall` to support yticklabels with boolean features ([fork58](https://github.com/dsgibbons/shap/pull/58) by dwolfeu).
- Prevent `TreeExplainer.__call__` from throwing ValueError when passed a pandas DataFrame containing Categorical columns ([fork88](https://github.com/dsgibbons/shap/pull/88) by thatlittleboy).
- Fixed sampling in `shap.datasets` to sample without replacement ([fork36](https://github.com/dsgibbons/shap/pull/36) by thatlittleboy).
- Fixed an `UnboundLocalError` problem arising from passing a dictionary input to `shap.plots.bar` ([3001](https://github.com/slundberg/shap/pull/3000) by thatlittleboy).
- Fixed tensorflow import issue with Pyspark when using `Gradient` ([2983](https://github.com/slundberg/shap/pull/2983) by skamdar).
- Fixed the aspect ratio of the colorbar in `shap.plots.heatmap`, and use the `ax` matplotlib API internally for plotting ([3040](https://github.com/slundberg/shap/pull/3040) by thatlittleboy).
- Fixed deprecation warnings for `numba>=0.44` ([fork9](https://github.com/dsgibbons/shap/pull/9) and [fork#68](https://github.com/dsgibbons/shap/pull/68) by connortann).
- Fixed deprecation warnings for `numpy>=1.24` from numpy types ([fork7](https://github.com/dsgibbons/shap/pull/7) by dsgibbons).
- Fixed deprecation warnings for `Ipython>=8` from `Ipython.core.display` ([fork13](https://github.com/dsgibbons/shap/pull/13) by thatlittleboy).
- Fixed deprecation warnings for `tensorflow>=2.11` from `tf.optimisers` ([fork16](https://github.com/dsgibbons/shap/pull/16) by simonangerbauer).
- Fixed deprecation warnings for `sklearn>=1.2` from `sklearn.linear_model` ([fork22](https://github.com/dsgibbons/shap/pull/22) by dsgibbons).
- Fixed deprecation warnings for `xgboost>=1.4` from `ntree_limit` in tree explainer ([2987](https://github.com/slundberg/shap/pull/2987) by adnene-guessoum).
- Fixed build on Windows and MacOS ([3015](https://github.com/slundberg/shap/pull/3015) by PrimozGodec; [#3028](https://github.com/slundberg/shap/pull/3028), [#3029](https://github.com/slundberg/shap/pull/3029) and [#3031](https://github.com/slundberg/shap/pull/3031) by connortann).
- Fixed creation of ragged arrays in `shap.explainers.Exact` ([3064](https://github.com/slundberg/shap/pull/3064) by connortann).

Changed

- Updates to docstrings of several `shap.plots` functions ([3003](https://github.com/slundberg/shap/pull/3003), [#3005](https://github.com/slundberg/shap/pull/3005) by thatlittleboy).

Removed

- Deprecated the Boston house price dataset ([fork38](https://github.com/dsgibbons/shap/pull/38) by thatlittleboy).
- Removed the unused `mimic.py` file and `MimicExplainer` code ([fork53](https://github.com/dsgibbons/shap/pull/53) by thatlittleboy).

Maintenance

- Fixed failing unit tests ([fork29](https://github.com/dsgibbons/shap/pull/29) by dsgibbons, [fork#20](https://github.com/dsgibbons/shap/pull/20) by simonangerbauer, [#3044](https://github.com/slundberg/shap/pull/3044) and [fork#24](https://github.com/dsgibbons/shap/pull/24) by connortann).
- Include CUDA GPU C extension files in the source distribution ([3009](https://github.com/slundberg/shap/pull/3009) by jklaise).
- Fixed installation of package via setuptools ([fork51](https://github.com/dsgibbons/shap/pull/51) by thatlittleboy).
- Introduced a minimal set of `ruff` linting ([fork25](https://github.com/dsgibbons/shap/pull/25), [fork#26](https://github.com/dsgibbons/shap/pull/26), [fork#27](https://github.com/dsgibbons/shap/pull/27), [#2973](https://github.com/slundberg/shap/pull/2973), [#2972](https://github.com/slundberg/shap/pull/2972) and [#2976](https://github.com/slundberg/shap/pull/2976) by connortann; [#2968](https://github.com/slundberg/shap/pull/2968), [#2986](https://github.com/slundberg/shap/pull/2986) by thatlittleboy).
- Updated project metadata to PEP 517 ([3022](https://github.com/slundberg/shap/pull/3022) by connortann).
- Introduced more thorough testing on CI against newer dependencies ([fork61](https://github.com/dsgibbons/shap/pull/61) and [#3017](https://github.com/slundberg/shap/pull/3017) by connortann)
- Reduced unit test time by ~5 mins ([3046](https://github.com/slundberg/shap/pull/3046) by connortann).
- Introduced fixtures for reproducible fuzz testing ([3048](https://github.com/slundberg/shap/pull/3048) by connortann).

Lots of bugs fixes and API improvements.

- Fixed rare bug with XGBoost model loading by TheZL lrjball
- Fixed the beeswarm plot so it does not modify the passed explanation object, ravwojdyla
- Automatic wheel building using GH actions by quantumtec
- GC collection for memory in KernelExplainer by Qingtian-Zou
- Fixed max_evals params for PartitionExplainer
- JIT optimize the PartitionExplainer
- Fix colorbar formatting issues SleepyPepperHead
- New benchmark notebooks
- Use display_data for plotting when possible yuuuxt
- Improved GPUTreeShap compilation and params RAMitchell
- Fix TF API change in DeepExplainer filusn
- Add torch tensor support for plots alexander-pv
- Switch to Github actions for testing instead of Travis
- New California demo dataset swalsh1123
- Fix waterfall plot bug RichardScottOZ
- Handle missing matplotlib installation klieret
- Add linearize link support for Additive explainer (Nandish Gupta)
- Fix exceptions to be more specific alexisdrakopoulos collinb9
- Add color map option for plotting tlabarta
- Release fixed numpy version requirement rmehyde
- And many other contributions kindly made by WeichenXu123 imatiach-msft zeshengli nkthiebaut songololo GiovannaNicora joshzwiebel Ashishbodla navdeep-G smathewmanuel ycouble anubhavmaity adityasaini70 ngupta20 jckkvs abs428 JulesCollenne Tiagosf00 javirandor and Thuener

This release contains many bugs fixes and lots of new functionality, specifically for transformer based NLP models. Some highlights include:
- New plots, bug fixes, docs, and features for NLP model explanations (see docs for details).
- important permutation explainer performance fix by sander-sn
- New joint scatter plots to plot many at once on the same y-scale
- better tree model memory usage by morriskurz
- new docs by coryroyce
- new wheel building by PrimozGodec
- dark mode improvements for the docs by gialmisi
- api tweaks by c56pony nsorros jebarb