chore(deps): update dependency shap to v0.51.0

[anaconda-renovate]

This PR contains the following updates:

Package	Update	Change
shap (changelog)	minor	==0.41.0 → ==0.51.0

renovate update details

Field	Value
manager	pip_requirements
categories	python
datasource	pypi
depName	shap
depType¹
packageName	shap
sourceUrl	https://github.com/shap/shap
updateType	minor
versioning	pep440

¹ only available for some managers

---

Release Notes

shap/shap (shap)

v0.51.0

Compare Source

What's Changed

Fixes

• fix: check first that the feature is not in the leaf node by @​Far-naz in #​4268
• Fix missing array to scalar conversion in MAPLE by @​Scienfitz in #​4285
• fix Python Version of Tree SHAP notebook by @​CloseChoice in #​4289
• Fix path-dependent SHAP NaN with small background datasets by @​tudstudent in #​4272
• Fix IndexError in format_value() when handling empty strings by @​Copilot in #​4238
• Fix test_scatter_categorical for pandas 3.0 compatibility by @​Copilot in #​4253
• Fix SamplingExplainer.explain for Series. by @​ljw20180420 in #​4200

Other Changes

• Add tests for fixed masker by @​CloseChoice in #​4216
• Add comprehensive type hints to production code by @​CloseChoice in #​4217
• unpin versions and pin numba, skip causalml test by @​CloseChoice in #​4235
• Clarify TreeExplainer binary classification returns different shapes per model by @​Copilot in #​4254
• Add tests for explainers by @​CloseChoice in #​4218
• Add Colab Notebook to test GPUTreeExplainer by @​CloseChoice in #​4266
• Fix spelling error in docs: perterbation to perturbation by @​laffertyryan0 in #​4275
• update test_scatter to work with latest xgboost by @​CloseChoice in #​4278
• add ai usage policy at appropriate place in contributing, mention contributing in readme by @​CloseChoice in #​4279
• deprecate testing of newer llvmlite versions on macos x64_86 by @​CloseChoice in #​4286

New Contributors

• @​ljw20180420 made their first contribution in #​4200
• @​Copilot made their first contribution in #​4238
• @​laffertyryan0 made their first contribution in #​4275
• @​tudstudent made their first contribution in #​4272
• @​Far-naz made their first contribution in #​4268
• @​Scienfitz made their first contribution in #​4285

Full Changelog: shap/shap@v0.50.0...v0.51.0

v0.50.0

Compare Source

What's Changed

• hand over threshold_types to GPUTreeExplainer by @​CloseChoice in #​4181
• Improve base_score assignment by @​lsdxp in #​4187
• test against python 3.14, remove support for python 3.9 and 3.10 by @​CloseChoice in #​4176
• Always force transformers label2id ids to integers by @​evamaxfield in #​4192
• Fix gpu tree explainer tests by @​CloseChoice in #​4199

New Contributors

• @​lsdxp made their first contribution in #​4187
• @​evamaxfield made their first contribution in #​4192

Full Changelog: shap/shap@v0.49.1...v0.50.0

v0.49.1

Compare Source

What's Changed

Fix broken v0.49.0 release.

The previous Release wasn't properly published due to HTTP errors on MacOS.

v0.48.0

Compare Source

What's Changed

Added

• Add CoalitionExplainer and add possibility of using Winter Values in Partition Explainer by @​CousinThrockmorton in #​3666
• Support and test against Python 3.13 by @​connortann in #​3861 and @​CloseChoice in #​4104
• Add Support for PyTorch Identity Layer by @​RoyiAvital in #​4028

Documentation

• Update Explaining a model that uses standardized features by @​randombenj in #​3903

Other Changes

• Changed alias by @​Ja-Tink in #​4049
• update javascript packages by @​CloseChoice in #​4067
• Fixed visual bug for small SHAP values by @​Ja-Tink in #​4053
• Fix summary_plot displays only one feature 4081 by @​CloseChoice in #​4087
• resolve threading warnings of regex library by @​emmanuel-ferdman in #​4084

New Contributors

• @​RoyiAvital made their first contribution in #​4028
• @​Ja-Tink made their first contribution in #​4049
• @​emmanuel-ferdman made their first contribution in #​4084
• @​randombenj made their first contribution in #​3903
• @​CousinThrockmorton made their first contribution in #​3666

Full Changelog: shap/shap@v0.47.2...v0.48.0

v0.47.2

Compare Source

What's Changed

Added

• Add experimental causalml support by @​alexander-pv in #​3273

Other Changes

• DOCS: clarity for partition tree explanation in Simple California Demo.ipynb by @​ethanknights in #​4027
• FIX: unique value jitter by @​fabianliebig in #​4041
• FIX: fix neutral language in SHAP value description by @​Hrafz in #​4058
• FIX regression test for javascript plotting compontents and add tests by @​CloseChoice in #​4060

New Contributors

• @​ethanknights made their first contribution in #​4027
• @​Hrafz made their first contribution in #​4058

Full Changelog: shap/shap@v0.47.1...v0.47.2

v0.47.1

Compare Source

Fixes

• Fix regression in summary violin plot by @​CloseChoice in #​4033
• Fix incorrect SHAP Values for Missing Data in new scikit versions for Tree Models by @​sunruslan in #​3998
• Fix issue with tight tolerances when calling check_additivity by @​adamwitmer in #​3993
• Fix AttributeError when extracting colors by @​fabianliebig in #​4017
• Fix additivity check failure uint32 overflow by @​arhall0 in #​4006

New Contributors

• @​adamwitmer made their first contribution in #​3993
• @​fabianliebig made their first contribution in #​4017
• @​sunruslan made their first contribution in #​3998
• @​arhall0 made their first contribution in #​4006

Full Changelog: shap/shap@v0.47.0...v0.47.1

v0.47.0

Compare Source

What's Changed

Breaking changes

• Add deprecation warning to legacy bar plot, add migration guide to new Explainer API by @​connortann in #​3739

Added

• Added categorical support for shap.plots.scatter by @​hypostulate in #​3706
• Introduce vmax parameter in image plot by @​sd3ntato in #​2848
• New plotting API for beeswarm to accept and return axes by @​chriscave in #​3561
• Enabeling to create a beeswarm figure without sum of other features by @​kalkairis in #​2225
• New interface to customise visualisations by @​connortann in #​3788
• Allow custom styles for bar plot by @​connortann in #​3849
• TreeExplainer numerical sensitivity by @​tylerjereddy in #​3990
• Faster non-tree KernelExplainer by @​tylerjereddy in #​3944

Fixed

• Fix logit errors in KernelExplainer by @​CloseChoice in #​3917
• Fix TypeError in summary_plot by @​bedapisl in #​3738
• Re-vendor colorconv from skimage 0.24.0 by @​connortann in #​3785
• Fix label option for multiple rows in shap.plots.image by @​SFatemehM in #​3636
• Fix transformers by @​costrau in #​3578
• Fix OpChain repr for kwargs-only operations by @​thatlittleboy in #​3838
• Fix the wrong figure for multiclass in summary plot by @​46319943 in #​3836
• Fix summary plot issue for multiclass case by @​CloseChoice in #​3925
• Fix colormaps by @​CloseChoice in #​3909

Documentation

• Fixed error in documentation of shap.datasets.communitiesandcrime by @​TommyGiak in #​3846
• Fix column indices in Understanding Tree SHAP notebook by @​operte in #​3749
• Reformat the scatter notebook in API example by @​Xovee in #​3752
• Improved typing and docs for scatter plot by @​connortann in #​3811
• Use intersphinx for some external links by @​thatlittleboy in #​3851
• Pin docs dependencies for reproducibility by @​connortann in #​3885
• Fix typo in force plot with LightGBM and description by @​davidefiocco in #​3962
• Fix: fixed markdown issue with some sections title in the introductio… by @​CSantos01 in #​3957
• Fix comment for beeswarm plot in intro notebook by @​davidefiocco in #​3960

Maintenance

• Fix: explicitly set matplotlib interpolation rcParams in tests by @​connortann in #​3953

Other Changes

• Skip sentiment analysis test on MacOS runners by @​connortann in #​3955
• Remove deprecated unused code _build_delta_masked_inputs and Explainer._compute_main_effects by @​connortann in #​3856
• Improve handling of the approximate parameter to TreeExplainer for consistency, and deprecate the argument in the explainer's init method by @​CloseChoice in #​3834
• Refactor feature_perturbation in Tree explainers by @​glemaitre in #​2624
• Test decision plot by @​CloseChoice in #​3720
• Bump ruff, fix rule E721 by @​connortann in #​3751
• Refactor plot utils and colors by @​thatlittleboy in #​3833
• Refactor and optimize explanation ops by @​thatlittleboy in #​3850
• Fix CI feedstock build by @​CloseChoice in #​3862
• Add error to multi output cohort call by @​CloseChoice in #​3870
• Fix typo in beeswarm.ipynb by @​kamurani in #​3900
• DeepExplainer docstring improvements by @​anitagraser in #​3892
• Clear plot before generating new summary plots to avoid overlapping color bars by @​chun61205 in #​3921
• Support rng for summary_plot by @​tylerjereddy in #​3945
• Minor speedups in non-tree KernelExplainer by @​tylerjereddy in #​3983

New Contributors

• @​bedapisl made their first contribution in #​3738
• @​operte made their first contribution in #​3749
• @​Xovee made their first contribution in #​3752
• @​hypostulate made their first contribution in #​3706
• @​SFatemehM made their first contribution in #​3636
• @​sd3ntato made their first contribution in #​2848
• @​chriscave made their first contribution in #​3561
• @​kalkairis made their first contribution in #​2225
• @​TommyGiak made their first contribution in #​3846
• @​46319943 made their first contribution in #​3836
• @​kamurani made their first contribution in #​3900
• @​anitagraser made their first contribution in #​3892
• @​chun61205 made their first contribution in #​3921
• @​davidefiocco made their first contribution in #​3962
• @​CSantos01 made their first contribution in #​3957
• @​Fredheda made their first contribution in #​3984
• @​tylerjereddy made their first contribution in #​3945

Full Changelog: shap/shap@v0.46.0...v0.47.0

v0.46.0

Compare Source

What's Changed

This release adds compatibility with recent version of numpy and tensorflow, and includes several bug fixes.

Added

• Added support for numpy 2, by @​connortann in #​3717 and @​paulbkoch in #​3704
• Added support for keras 3 and tensorflow 2.16 by @​CloseChoice in #​3677

Changed

• Removed the deprecated auto_size_plot parameter to shap.summary_plot().

Fixed

• Fixed issue explaining models trained with float16 mixed precision by @​CloseChoice in #​3652
• Fixed deserialization bug with XGBRegressor models by @​CloseChoice in #​3669

Plus several further documentation and code quality improvements.

New Contributors

• @​LetiP made their first contribution in #​3685
• @​paulbkoch made their first contribution in #​3704

Full Changelog: shap/shap@v0.45.1...v0.46.0

v0.45.1

Compare Source

This is a patch release with a couple of bug fixes. In particular, fixes a bug relating to loading of XGBoost models with exponential losses.

What's Changed

Added

• Added selu activation for pytorch deep explainer by @​CloseChoice in #​3617
• Added "ax" option to heatmap plotting function by @​sroener in #​3571

Changed

• Removed unused "display" parameters from dataset functions by @​LakshmanKishore in #​3543

Fixed

• Fixed loading of XGBoost models with expeonential lossesby @​CloseChoice in #​3616
• Fixed call interface for the deep explainer by @​CloseChoice in #​3558
• Fixed use of Falcon language model for text generation by @​CloseChoice in #​3592
• Fixed lightgbm compilation (macOS Workflow) by @​bewygs in #​3632
• Fixed loading of XGBoost models with exponential losses by @​CloseChoice in #​3616

Plus several documentation and maintenance updates by @​bewygs , @​CloseChoice , @​Hugh-OBrien

New Contributors

• @​sroener made their first contribution in #​3571
• @​Hugh-OBrien made their first contribution in #​3604
• @​bewygs made their first contribution in #​3632

Full Changelog: shap/shap@v0.45.0...v0.45.1

v0.45.0

Compare Source

This is a fairly significant release containing a number of breaking changes.

Thank you to a number of new contributors for their contributions to this release! We are eager to grow the pool of maintainers, so please do get in touch on #​3559 if you are interested in being part of the team.

What's Changed

Breaking changes

• Dropped support for 3.8 in #​3414
• Changed type and shape of returned SHAP values in some cases, to be consistent with model outputs. SHAP values for models with multiple outputs are now np.ndarray rather than list, by @​CloseChoice in #​3318
• Removed deprecated feature_dependence parameters in TreeExplainer and LinearExplainer by @​thatlittleboy in #​3340
• Removed deprecated alias for Coefficient by @​connortann in #​3511

Added

• Added support for python 3.12 by @​connortann in #​3414
• Added support for GPU build on recent CUDA versions by @​trivialfis in #​3462
• 2x import time speedup via lazy importing of pytorch by @​connortann in #​3533
• Added support returning the matplotlib figure in bar plots by @​richarddli in #​3494
• Added selu activation for tensorflow deep explainer by @​CloseChoice in #​3504
• Added support for special characters in catboost models by @​CloseChoice in #​3506
• Added ability to control marker size in beeswarm plots by @​MonoHue in #​3530

Fixed

• Fixed XGBoost model load by @​trivialfis in #​3462
• Fixed text masking with certain tokenizers by @​costrau in #​3536
• Fixed issue with KernelExplainer when explaining tensorflow models by @​connortann in #​3542
• Fixed force_plot contribution threshold for negative contributions by @​connortann in #​3547
• Removed overwrite of default warning filter or formatter by @​connortann in #​3514

.. plus a large number of documentation, testing and other maintenance updates by @​CloseChoice , @​yuanx749 , @​LakshmanKishore and others.

New Contributors

• @​richarddli made their first contribution in #​3494
• @​yuanx749 made their first contribution in #​3458
• @​LakshmanKishore made their first contribution in #​3393
• @​trivialfis made their first contribution in #​3462
• @​DanGolding made their first contribution in #​3526
• @​MonoHue made their first contribution in #​3530
• @​costrau made their first contribution in #​3536

Full Changelog: shap/shap@v0.44.1...v0.45.0

v0.44.1

Compare Source

Patch release to fix an issue with the display of force plots.

Fixed

• Fixed HTML issue affecting display of force plots by @​CloseChoice in #​3464
• Fixed calculation of interactions values for catboost regressors by @​CloseChoice in #​3459
• Update XGBoost parsing to use ubjson format, replacing deprecated binary format by @​CloseChoice in #​3345

Other

• Further improvements to documentation

Full Changelog: shap/shap@v0.44.0...v0.44.1

v0.44.0

Compare Source

This release contains a number enhancements and bug fixes.

What's Changed

Added

• Faster and more stable linear solver in KernelShap by @​lorentzenchr in #​3271
• Enabled passing of ax to group_difference() plot by @​mtlulka in #​3355
• Added support for Explanation.display_data in bar plot by @​fountaindive in #​3386
• Improved build messages when building from source by @​connortann in #​3403

Fixed

• Fixed CatboostClassifier explanations with feature interactions on Windows by @​CloseChoice in #​3325
• Fixed passing of Xgboost model parameters to xgboost.DMatrix by @​vancromy in #​3314
• Explicit specification of xgboost>=1.4 constraint by @​mtlulka in #​3352
• Fixed conversion of DMatrix to CSR matrix by @​thatlittleboy in #​3359
• Removed deprecated use_line_collection in dependence_plot by @​CloseChoice in #​3369
• Fixed bug relating to array reshaping in scatter plots by @​SomeUserName1 in #​2799

Documentation

• A large number of example notebooks fixed and updated by @​connortann, @​znacer , @​thatlittleboy, @​CloseChoice and @​stompsjo

New Contributors

• @​vancromy made their first contribution in #​3314
• @​lorentzenchr made their first contribution in #​3271
• @​mtlulka made their first contribution in #​3352
• @​fountaindive made their first contribution in #​3386
• @​SomeUserName1 made their first contribution in #​2799
• @​stompsjo made their first contribution in #​3391

Full Changelog: shap/shap@v0.43.0...V0.44.0

v0.43.0

Compare Source

What's Changed

This release contains a number of bug fixes and improvements.

Following the NEP 29 deprecation policy, this release drops support for python 3.7.

Breaking changes

• Removed the deprecated Boston dataset by @​thatlittleboy in #​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 #​3121

Added

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

Fixed

• Fixed segmentation faults on MacOS with lightgbm tests (with newer libomp versions) by @​thatlittleboy in #​3093
• Support LightGBM ensemble containing single leaf trees (stump) by @​thatlittleboy in #​3094
• Fixed conversion DataFrame to ndarray for Explanation.data by @​danieleongari in #​3131
• Fixed waterfall plot on explanations of sklearn tree models by @​connortann in #​3138
• Fixed pandas input for gradient explainer by @​Koen-Git in #​3153
• Fixed slicing of feature_names in Explanation objects with square .values by @​thatlittleboy in #​3126
• Correct xlim in force_matplotlib in cases where the signs of force are all the same by @​zaburo-ch in #​2839
• Fixed ngboost explanations when col_sample < 1 by @​CloseChoice in #​3294
• Fixed torch additivity check in PyTorch DeepExplainer by @​noxthot in #​3281
• Replaced print statements with warnings in DeepExplainer by @​znacer in #​3264
• Replace deprecated register_backward_hook() by @​noxthot in #​3259
• Fixed deprecated use of xgboost early_stopping_rounds by @​CloseChoice in #​3306
• Fixed 3rd party deprecation warnings: numba, xgboost, typing, distutils by @​connortann in #​3084
• Updated the Javascript bundle to update deprecated dependencies by @​connortann in #​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 #​3062
• @​znacer made their first contribution in #​3112
• @​danieleongari made their first contribution in #​3131
• @​Koen-Git made their first contribution in #​3153
• @​pre-commit-ci made their first contribution in #​3173
• @​owenlamont made their first contribution in #​3199
• @​arshiaar made their first contribution in #​3201
• @​dsgibbons made their first contribution in #​3200
• @​noxthot made their first contribution in #​3265
• @​zaburo-ch made their first contribution in #​2839
• @​CloseChoice made their first contribution in #​3282

Full Changelog: shap/shap@v0.42.1...v0.43.0

v0.42.1

Compare Source

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

Added

• Added wheels for linux:aarch64 and macos:arm64 by @​PrimozGodec in slundberg#3078 and @​connortann in slundberg#3083.

Fixed

• Fixed circular import issues with shap.benchmark by @​thatlittleboy in slundberg#3076.
• Fixed TestPyPI releases workflow by @​connortann in slundberg#3068
• Fix further flaky tests by @​thatlittleboy in slundberg#3073
• Fix shap.summary_plot to work with matplotlib 3.6.0 by @​jklaise in slundberg#2697
• Fix benchmark top-level import by @​thatlittleboy in slundberg#3076
• Fix ipython import warning from top-level shap import by @​connortann in slundberg#3090

Full Changelog: shap/shap@v0.42.0...v0.42.1

v0.42.0

Compare Source

This release incorporates many changes that were originally contributed by the SHAP community via @​dsgibbons's Community Fork, which has now been merged into the main shap repository. PRs from this origin are labelled here as fork#123.

This will be the last release that supports python 3.7.

Added

• Added support for python 3.11 (fork#72 by @​connortann).
• Added n_points parameter to all functions in shap.datasets (fork#39 by @​thatlittleboy).
• Added __call__ to KernelExplainer (#​2966 by @​dwolfeu).
• Added contributing guidelines (#​2996 by @​connortann).

Fixed

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

Changed

• Updates to docstrings of several shap.plots functions (#​3003, #​3005 by @​thatlittleboy).

Removed

• Deprecated the Boston house price dataset (fork#38 by @​thatlittleboy).
• Removed the unused mimic.py file and MimicExplainer code (fork#53 by @​thatlittleboy).

Maintenance

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

---

Configuration

📅 Schedule: (in timezone UTC)

• Branch creation
  • "every weekday"
• Automerge
  • At any time (no schedule defined)

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.

---

• If you want to rebase/retry this PR, check this box

---

This PR has been generated by Renovate Bot.

[anaconda-renovate]

Edited/Blocked Notification

Renovate will not automatically rebase this PR, because it does not recognize the last commit author and assumes somebody else may have edited the PR.

You can manually request rebase by checking the rebase/retry box above.

⚠️ Warning: custom changes will be lost.