Update python-machine-learning-libs

[renovate]

This PR contains the following updates:

Package	Change	Age	Confidence
optuna	==4.6.0 → ==4.7.0
scikit-learn (changelog)	==1.7.2 → ==1.8.0
shap (changelog)	==0.49.1 → ==0.50.0
umap-learn	==0.5.9.post2 → ==0.5.11

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Release Notes

optuna/optuna (optuna)

v4.7.0

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This is the release note of v4.7.0.

Highlights

Two New Multi-Objective Samplers Added to OptunaHub!

@​hrntsm introduces two new multi-objective samplers—SPEA-II (Strength Pareto Evolutionary Algorithm 2) and HypE (Hypervolume Estimation Algorithm)—to OptunaHub. SPEA-II is an improved multi-objective evolutionary algorithm that differs from NSGA-II in its selection mechanism. HypE is a fast, hypervolume-based evolutionary algorithm designed for many-objective optimization problems. Please refer to the following pages for more details:

• SPEA-II: https://hub.optuna.org/samplers/speaii/
• HypE: https://hub.optuna.org/samplers/hype/

PedAnovaImportanceEvaluator Now Supports Local Hyperparameter Importance Computation

The target_quantile and region_quantile arguments have been introduced to PedAnovaImportanceEvaluator. This change allows you to investigate local hyperparameter importance rather than the global one with region_quantile < 1.0. See the original paper for the technical details.

Enhancements

• Introduce stacklevel-aware custom warnings (#​6293)
• Cache distributions to skip consistency check (#​6301)
• Add warnings when JournalStorage lock acquisition is delayed (#​6361)
• Add support for local HPI in PED-ANOVA (#​6362)

Bug Fixes

• Fix log PDF of discrete trunc log-norm distribution for TPESampler (#​6258)
• Fix coefficient in PED-ANOVA (#​6358)
• Fix GPSampler crash when default torch device is CUDA (#​6397, thanks @​Quant-Quasar!)

Documentation

• Add SECURITY.md (#​6317)
• Add a note for future dev of exclusive HV (#​6318)
• Update GPSampler documentation to include D-BE optimization details (#​6347, thanks @​Kaichi-Irie!)
• Revert PR #​6354 to enable -W option on Sphinx build (#​6373)

Examples

• Disable scheduled runs for PyTorch and visualization temporarily (optuna/optuna-examples#337)
• Fix skorch example: Replace unavailable OpenML MNIST (optuna/optuna-examples#338, thanks @​sotagg!)
• Pin minio version to <=7.2.18 to fix CI & stop daily CI running (optuna/optuna-examples#339)
• fix spark example (optuna/optuna-examples#342, thanks @​fritshermans!)
• Pin scikit-learn to < 1.6.0 for lightgbm (optuna/optuna-examples#343)
• Remove python 3.9 due to EOL Status (optuna/optuna-examples#344, thanks @​ParagEkbote!)
• Add IPython as a dependency of fastai example (optuna/optuna-examples#347)

Tests

• Fix TC006 violation in tests/visualization_tests/test_utils.py (#​6387, thanks @​jiayusu!)

Code Fixes

• Replace .format() with f-string in _setup_studies (#​6326, thanks @​haitham404!)
• Update _upload.py for TYPE_CHECKING (#​6327, thanks @​satyarth7srivastava!)
• Replace .format() with f-string in progress_bar.py (#​6328, thanks @​Nayil97!)
• Use f-strings in optuna/samplers/_cmaes.py (#​6331, thanks @​swativdusane!)
• Replace .format() with f-string in _parallel_coordinate.py (#​6333, thanks @​satyarth7srivastava!)
• Refactor/fstring storage rdb (#​6336, thanks @​gadmin7!)
• Migrate to ruff from black/blackdoc/isort/flake8 (#​6341)
• Replace .format with f-strings in optuna/importance/_base (#​6342, thanks @​VihaanMotwani!)
• updated _terminator_improvement.py for TYPE_CHECKING (#​6343, thanks @​satyarth7srivastava!)
• Replace .format with f-string in _param_importances.py (#​6345, thanks @​Harshadev-24!)
• Replace .format() with f-strings in several modules (#​6348, thanks @​varundevr!)
• Replace more .format() calls with f-strings (#​6349, thanks @​varundevr!)
• Replace .format with f-string in tutorial/20_recipes/004_cli.py (#​6350, thanks @​RektPunk!)
• Replace .format with f-string in optuna/study/_optimize.py (#​6351, thanks @​RektPunk!)
• Format optuna/ files with Ruff (#​6352)
• Refactor: Use f-string in 001_rdb.py (#​6356, thanks @​sotagg!)
• Format tests/ and tutorials/ files with Ruff (#​6360)
• Remove redundant _color_supported() check (#​6363)
• Add StorageTestCase class in optuna.testing package (#​6369)
• Change string formatting in optuna/pruners/_hyperband.py (#​6370, thanks @​eleannapapaio!)
• Refactor test_study.py to use f-string instead of .format() (#​6372, thanks @​nepersoned!)
• Fix mypy error for np.select (#​6374)
• Change string formatting for _successive_halving.py (#​6375, thanks @​spenam!)
• Fix type annotations for optuna/trial/_frozen.py (#​6377, thanks @​spenam!)
• fix type annotations for optuna/study/study.py (#​6378, thanks @​spenam!)
• Fix type annotations for tests/study_tests/test_study.py (#​6379, thanks @​spenam!)
• Move type-only imports to TYPE_CHECKING in test_visualizations.py (#​6380, thanks @​Sip4818!)
• Move type-only imports to TYPE_CHECKING in _constrained_optimization.py (#​6381, thanks @​Sip4818!)
• Replace format with f-string (#​6383, thanks @​varundevr!)
• Move type-only imports to TYPE_CHECKING in _multi_objective.py (#​6385, thanks @​Sip4818!)
• Move FrozenTrial import under TYPE_CHECKING for _study_summary.py file (#​6386, thanks @​Sip4818!)
• Move type-check imports to TYPE_CHECKING in optuna/terminator/callback.py (#​6388, thanks @​Sip4818!)
• Using f-string instead of .format() (#​6389, thanks @​Lakshman142!)
• Use f-strings in optuna/_experimental.py (#​6390, thanks @​Rohan0497!)
• Fix invalid StorageTestCase scenarios involving trial state and values (#​6391)
• Move type-hint import inside Type-Checking block in optuna\terminator\erroreval.py (#​6395, thanks @​Sip4818!)
• Move type-check imports to TYPE_CHECKING in optuna\terminator\improvement\emmr.py (#​6396, thanks @​Sip4818!)
• Move typing-only imports under TYPE_CHECKING in matplotlib/_slice.py (#​6399, thanks @​kapishyadav!)
• Use logger.warning instead of optuna_warn for lock-acquisition delay notifications (#​6400)
• Update string formatting in optuna/samplers/_grid.py (#​6401, thanks @​kapishyadav!)
• Updating storages/_in_memory.py to use f-strings (#​6404, thanks @​jrings!)
• Move type-hint imports into type-checking block in optuna\terminator\improvement\evaluator.py (#​6405, thanks @​Sip4818!)
• Move type-hint imports into type-checking block in median_erroreval.py (#​6408, thanks @​Sip4818!)
• Replace .format() with f-string in _rank.py (#​6409, thanks @​jwalith!)
• Replace .format() with f-string in test_hyperband.py (#​6411, thanks @​Banjiola!)
• Replace .format() with f-string in _fixed.py (#​6412, thanks @​VedantMadane!)

Continuous Integration

• Fix for CI (optuna/optuna-integration#258)
• Add ipython as a dependency of fastai (optuna/optuna-integration#261)
• Remove FastAIV2PruningCallback from docs to resolve warning (optuna/optuna-integration#264)
• Dispose SQLAlchemy's engine in storage_tests/test_with_server.py (#​6330)
• Dispose SQLAlchemy's engine in storage_tests/test_cached_storage.py (#​6337)
• Dispose SQLAlchemy's engine in storage_tests/rdb_tests/test_storage.py (#​6338)
• Support Python 3.14 (#​6339)
• Temporarily disable -W option on Sphinx build (#​6354)

Other

• Bump up version (optuna/optuna-integration#256)
• Bump up version number to 4.7.0 (optuna/optuna-integration#262)
• Bump up to the version number v4.7.0.dev (#​6325)
• Update the news section on README (#​6335)
• Remove Codecov usage (#​6340)
• Remove formats.sh and tidy up CONTRIBUTING.md (#​6353)
• Remove asv and the speed benchmark workflow (#​6393)
• Bump up version to v4.7.0 (#​6413)

Thanks to All the Contributors!

This release was made possible by the authors and the people who participated in the reviews and discussions.

@​Alnusjaponica, @​Banjiola, @​Harshadev-24, @​HideakiImamura, @​Kaichi-Irie, @​Lakshman142, @​Nayil97, @​ParagEkbote, @​Quant-Quasar, @​RektPunk, @​Rohan0497, @​Sip4818, @​VedantMadane, @​VihaanMotwani, @​c-bata, @​eleannapapaio, @​fritshermans, @​fusawa-yugo, @​gadmin7, @​gen740, @​haitham404, @​jiayusu, @​jrings, @​jwalith, @​kAIto47802, @​kapishyadav, @​nabenabe0928, @​nepersoned, @​not522, @​nzw0301, @​satyarth7srivastava, @​sawa3030, @​sotagg, @​spenam, @​swativdusane, @​toshihikoyanase, @​varundevr, @​y0z

scikit-learn/scikit-learn (scikit-learn)

v1.8.0

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We're happy to announce the 1.8.0 release.

You can read the release highlights under https://scikit-learn.org/stable/auto_examples/release_highlights/plot_release_highlights_1_8_0.html and the long version of the change log under https://scikit-learn.org/stable/whats_new/v1.8.html

This version supports Python versions 3.11 to 3.14 and features support of free-threaded CPython.

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds can be installed using:

conda install -c conda-forge scikit-learn

shap/shap (shap)

v0.50.0

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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

lmcinnes/umap (umap-learn)

v0.5.11

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