shap 0.52.0

v0.52.0

on Python PyPI

What's Changed

Highlights

• Native bindings rewritten with nanobind, and the build system migrated
  from setup.py to scikit-build-core + CMake. The Cython
  _kernel_lib.pyx and the existing _cext / _cext_gpu modules are now
  built as nanobind extensions, and MANIFEST.in / setup.py have been
  removed in favor of a pyproject.toml-driven build. (#4366, by
  @CloseChoice and @daidahao and @claude)
• Minimum dependency versions raised to follow SPEC 0. (#4310, by @CloseChoice)

Enhancements

• Log an INFO message when background data is sub-sampled (closes #3461).
  (#4294, by @Ebube22)
• Add cross-links between the API Reference and API Examples pages.
  (#4329, by @Abhishek9639)
• Drop the unused typing-extensions dependency. (#4629, by @samudraneel05)

Bug Fixes

• Improve GPU TreeExplainer parity: preserve XGBoost default/missing child
  routing so NaN values follow the same branch as the source model, preserve
  vector-valued XGBoost base_score values (fixing multiclass additivity
  offsets), and tighten categorical handling so sklearn models with
  enable_categorical=True raise the existing unsupported-categorical error
  even when the booster does not expose feature_types. (#4997, by
  @RAMitchell)
• TreeExplainer no longer crashes with pandas nullable dtypes.
  (#4298, by @tudstudent)
• Fix NameError when with_binary=False and with_cuda=True by
  initializing compile_args. (#4322, by @mohityadav8)
• Text plot colors render correctly by converting NumPy types to float.
  (#4332, by @Saloni-0465)
• Assign the result of np.flipud so it is no longer a no-op in
  AdditiveForceArrayVisualizer. (#4343, by @Mahaveerjain-18)
• Use isinstance() instead of is for type checks. (#4373, by @divyam-jha123)
• Record 'sample' in Explanation.op_history instead of '__getitem__'.
  (#4376, by @tarun-227)
• Move the unreachable large-dataset warning into the interventional branch.
  (#4392, by @Mahaveerjain-18)
• Fix "structure of inputs doesn't match the expected structure".
  (#4410, by @shaivimalik)
• Fix the return value from is_color_map() in plots/_beeswarm.py.
  (#4421, by @maniktyagi04)
• Suppress the UserWarning when LGBMRegressor was fitted with feature
  names. (#4422, by @shaivimalik)
• Correct max_evals calculation in PermutationExplainer.shap_values().
  (#4434, by @AftAb-25)
• Fix incorrect measure calls in benchmark/metrics.py.
  (#4447, by @Jiya873)
• Handle zero division in the heatmap when all SHAP values are zero.
  (#4449, by @BaibhavKundu2005)
• Correct file path handling in make_dir (image.py).
  (#4501, by @Abhishek-Kumar-Rai5)
• Use isinstance() instead of type() is for tuple checks.
  (#4508, by @neha222222)
• Warn when the covariance matrix is singular in LinearExplainer.
  (#4471, by @BaibhavKundu2005)
• Remove a debug print and a typo in serializable.
  (#4336, by @dhiraj-143r)

Maintenance

• Fix a NumPy deprecation warning in the coalition explainer.
  (#4291, by @CloseChoice)
• Fix deprecated NumPy dtype aliases in test_kernel.py.
  (#4302, by @peteroyce)
• Replace the deprecated input_shape kwarg with an Input layer in tests.
  (#4301, by @kvr06-ai)
• Replace deprecated return_all_scores with top_k=None (#3974).
  (#4393, by @shauryam2807)
• Remove dead code in utils/_keras.py (unused and broken on Keras 3).
  (#4625, by @SuMayaBee)
• Remove the dead __check_cache function and stale cache variables in
  benchmark. (#4485, by @dhiraj-143r)
• Update bundled JS. (#4308, by @CloseChoice)

Type Hints

• Add type hints for explainers.other._random. (#4436, by @SarthakB11)

Tests

• Add SHAP values baselines. (#4307, by @CloseChoice)
• Add more exact explainer
  #4366tests. (#4312, by @CloseChoice)
• Re-enable causalml tests. (#4311, by @dhiraj-143r)
• Make force plot tests deterministic to fix macOS flakiness (#4102).
  (#4315, by @Abhishek9639)
• Add a new exact explainer test. (#4364, by @CloseChoice)
• Use the default matplotlib style for tests. (#4330, by @Anushreebasics)
• Restore pytest discovery for shap.actions. (#4350, by @JRV7903)
• Improve test coverage for the Action base class. (#4514, by @Jiya873)
• Add tests in tests/explainers/test_linear.py. (#4416, by @naxatra2)
• Increase test coverage for shap/explainers/other/_treegain.py.
  (#4427, by @rupeshca007)

Documentation

• Update LightGBM links. (#4296, by @jameslamb)
• Fix Python installation version from 3.11 to 3.12. (#4319, by @kronzter)
• Fix a broken link. (#4400, by @Jiya873)
• Update the Iris classification notebook to use the modern SHAP API.
  (#4318, by @JRV7903)
• Fix typos in the heatmap notebook. (#4359, by @Bot87Ever)
• Reformat the waterfall notebook. (#4378, by @justin212407)
• Improve clarity and documentation in the sentiment analysis notebook.
  (#4397, by @24f3004086)
• Improve the embedding plot docstring. (#4438, by @Jiya873)
• Modernize the "Fitting a Linear Simulation with XGBoost" notebook.
  (#4428, by @vibhor-5)
• Fix spelling errors in source code docstrings and comments.
  (#4446, by @rupeshca007)
• Clarify the expected_value math formula in TreeExplainer (#4414).
  (#4418, by @DashratRajpurohit)

New Contributors

• @daidahao made their first contribution in #4366
• @peteroyce made their first contribution in #4302
• @kvr06-ai made their first contribution in #4301
• @dhiraj-143r made their first contribution in #4311
• @Abhishek9639 made their first contribution in #4315
• @kronzter made their first contribution in #4319
• @Jiya873 made their first contribution in #4400
• @shauryam2807 made their first contribution in #4393
• @Ebube22 made their first contribution in #4294
• @JRV7903 made their first contribution in #4318
• @mohityadav8 made their first contribution in #4322
• @Saloni-0465 made their first contribution in #4332
• @Anushreebasics made their first contribution in #4330
• @Bot87Ever made their first contribution in #4359
• @SuMayaBee made their first contribution in #4625
• @divyam-jha123 made their first contribution in #4373
• @justin212407 made their first contribution in #4378
• @samudraneel05 made their first contribution in #4629
• @Mahaveerjain-18 made their first contribution in #4392
• @24f3004086 made their first contribution in #4397
• @shaivimalik made their first contribution in #4410
• @tarun-227 made their first contribution in #4376
• @maniktyagi04 made their first contribution in #4421
• @naxatra2 made their first contribution in #4416
• @rupeshca007 made their first contribution in #4427
• @vibhor-5 made their first contribution in #4428
• @SarthakB11 made their first contribution in #4436
• @AftAb-25 made their first contribution in #4434
• @DashratRajpurohit made their first contribution in #4418
• @Abhishek-Kumar-Rai5 made their first contribution in #4501
• @BaibhavKundu2005 made their first contribution in #4449
• @neha222222 made their first contribution in #4508

Full Changelog: v0.51.0...v0.52.0