Scikit-survival

This release adds support for scikit-learn 1.2 and drops support for previous versions.

Enhancements

- Raise more informative error messages when a parameter does not have a valid type/value (see [sklearn23462](https://github.com/scikit-learn/scikit-learn/issues/23462)).
- Add positive and random_state parameters to [sksurv.linear_model.IPCRidge](https://scikit-survival.readthedocs.io/en/v0.20.0/api/generated/sksurv.linear_model.IPCRidge.html#sksurv.linear_model.IPCRidge).

Documentation

- Update API docs based on scikit-learn 1.2 (where applicable).

Backwards incompatible changes

- To align with the scikit-learn API, many parameters of estimators must be provided with their names, as keyword arguments, instead of positional arguments.

- Remove deprecated `normalize` parameter from [sksurv.linear_model.IPCRidge](https://scikit-survival.readthedocs.io/en/v0.20.0/api/generated/sksurv.linear_model.IPCRidge.html#sksurv.linear_model.IPCRidge).

- Remove deprecated `X_idx_sorted` argument from [sksurv.tree.SurvivalTree.fit()](https://scikit-survival.readthedocs.io/en/v0.20.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree.fit).

- Setting `kernel="polynomial"` in [sksurv.svm.FastKernelSurvivalSVM](https://scikit-survival.readthedocs.io/en/v0.20.0/api/generated/sksurv.svm.FastKernelSurvivalSVM.html#sksurv.svm.FastKernelSurvivalSVM), [sksurv.svm.HingeLossSurvivalSVM](https://scikit-survival.readthedocs.io/en/v0.20.0/api/generated/sksurv.svm.HingeLossSurvivalSVM.html#sksurv.svm.HingeLossSurvivalSVM), and [sksurv.svm.MinlipSurvivalAnalysis](https://scikit-survival.readthedocs.io/en/v0.20.0/api/generated/sksurv.svm.MinlipSurvivalAnalysis.html#sksurv.svm.MinlipSurvivalAnalysis) has been replaced with `kernel="poly"`.

**Full Changelog**: https://github.com/sebp/scikit-survival/compare/v0.19.0.post1...v0.20.0

This release raises the install requirement of scikit-learn to 1.1.2 to avoid binary incompatibility with previous releases (316).

**Full Changelog**: https://github.com/sebp/scikit-survival/compare/v0.19.0...v0.19.0.post1

This release adds [sksurv.tree.SurvivalTree.apply()](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree.apply) and [sksurv.tree.SurvivalTree.decision_path()](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree.decision_path), and support for sparse matrices to [sksurv.tree.SurvivalTree](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree). Moreover, it fixes build issues with scikit-learn 1.1.2 and on macOS with ARM64 CPU.

Bug fixes
- Fix build issue with scikit-learn 1.1.2, which is binary-incompatible with previous releases from the 1.1 series.
- Fix build from source on macOS with ARM64 by specifying numpy 1.21.0 as install requirement for that platform (313).

Enhancements

- [sksurv.tree.SurvivalTree](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree): Add [sksurv.tree.SurvivalTree.apply()](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree.apply) and [sksurv.tree.SurvivalTree.decision_path()](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree.decision_path) (290).
- [sksurv.tree.SurvivalTree](https://scikit-survival.readthedocs.io/en/v0.19.0/api/generated/sksurv.tree.SurvivalTree.html#sksurv.tree.SurvivalTree): Add support for sparse matrices (290).

**Full Changelog**: https://github.com/sebp/scikit-survival/compare/v0.18.0...v0.19.0

This release adds support for scikit-learn 1.1, which includes more informative error messages.
Support for Python 3.7 has been dropped, and the minimum supported versions of dependencies are updated to
- numpy 1.17.3
- Pandas 1.0.5
- scikit-learn 1.1.0
- scipy 1.3.2

Enhancements
- Add ``n_iter_`` attribute to all estimators in [sksurv.svm](https://scikit-survival.readthedocs.io/en/v0.18.0/api/svm.html#mod-svm) (277).
- Add ``return_array`` argument to all models providing
``predict_survival_function`` and ``predict_cumulative_hazard_function`` (268).

Deprecations
- The ``loss_`` attribute of [ComponentwiseGradientBoostingSurvivalAnalysis](https://scikit-survival.readthedocs.io/en/latest/api/generated/sksurv.ensemble.ComponentwiseGradientBoostingSurvivalAnalysis.html#sksurv.ensemble.ComponentwiseGradientBoostingSurvivalAnalysis) and [GradientBoostingSurvivalAnalysis](https://scikit-survival.readthedocs.io/en/v0.18.0/api/generated/sksurv.ensemble.GradientBoostingSurvivalAnalysis.html#sksurv.ensemble.GradientBoostingSurvivalAnalysis) has been deprecated.
- The default for the ``max_features`` argument has been changed from ``'auto'`` to ``'sqrt'`` for [RandomSurvivalForest](https://scikit-survival.readthedocs.io/en/v0.18.0/api/generated/sksurv.ensemble.RandomSurvivalForest.html#sksurv.ensemble.RandomSurvivalForest) and [ExtraSurvivalTrees](https://scikit-survival.readthedocs.io/en/v0.18.0/api/generated/sksurv.ensemble.ExtraSurvivalTrees.html#sksurv.ensemble.ExtraSurvivalTrees). ``'auto'`` and ``'sqrt'`` have the same effect.

**Full Changelog**: https://github.com/sebp/scikit-survival/compare/v0.17.2...v0.18.0

This release fixes several issues with packaging scikit-survival.

Bug fixes

- Added backward support for gcc-c++ by navashiva (255).
- Do not install C/C++ and Cython source files.
- Add `packaging` to build requirements in `pyproject.toml`.
- Exclude generated API docs from source distribution.
- Add Python 3.10 to classifiers.

Documentation

- Use [permutation_importance](https://scikit-learn.org/stable/modules/generated/sklearn.inspection.permutation_importance.html#sklearn.inspection.permutation_importance) from sklearn instead of eli5.
- Build documentation with Sphinx 4.4.0.
- Fix missing documentation for classes in `sksurv.meta`.

New Contributors
- navashiva made their first contribution in https://github.com/sebp/scikit-survival/pull/255

**Full Changelog**: https://github.com/sebp/scikit-survival/compare/v0.17.1...v0.17.2

This release adds support for Python 3.10.

**Full Changelog**: https://github.com/sebp/scikit-survival/compare/v0.17.0...v0.17.1