scikit-survival 0.23.0__tar.gz → 0.24.0__tar.gz

{scikit_survival-0.23.0/scikit_survival.egg-info → scikit_survival-0.24.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: scikit-survival
-Version: 0.23.0
+Version: 0.24.0
 Summary: Survival analysis built on top of scikit-learn
 Author-email: Sebastian Pölsterl <sebp@k-d-w.org>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -694,13 +694,13 @@ Classifier: Programming Language :: C++
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: COPYING
 Requires-Dist: ecos
@@ -708,9 +708,9 @@ Requires-Dist: joblib
 Requires-Dist: numexpr
 Requires-Dist: numpy
 Requires-Dist: osqp!=0.6.0,!=0.6.1
-Requires-Dist: pandas>=1.0.5
+Requires-Dist: pandas>=1.4.0
 Requires-Dist: scipy>=1.3.2
-Requires-Dist: scikit-learn<1.6,>=1.4.0
+Requires-Dist: scikit-learn<1.7,>=1.6.1
 Provides-Extra: dev
 Requires-Dist: black[jupyter]; extra == "dev"
 Requires-Dist: build; extra == "dev"
@@ -736,10 +736,10 @@ Requires-Dist: sphinx-copybutton~=0.5.2; extra == "docs"
 Provides-Extra: nbval
 Requires-Dist: ipykernel; extra == "nbval"
 Requires-Dist: ipython!=8.7.0; extra == "nbval"
-Requires-Dist: matplotlib~=3.6.2; extra == "nbval"
+Requires-Dist: matplotlib~=3.9.0; extra == "nbval"
 Requires-Dist: nbformat; extra == "nbval"
 Requires-Dist: nbval>=0.10.0; extra == "nbval"
-Requires-Dist: seaborn~=0.11.2; extra == "nbval"
+Requires-Dist: seaborn~=0.13.2; extra == "nbval"
 
 |License| |Docs| |DOI|
 
@@ -775,14 +775,14 @@ this unique characteristic of such a dataset into account.
 Requirements
 ============
 
-- Python 3.9 or later
+- Python 3.10 or later
 - ecos
 - joblib
 - numexpr
 - numpy
 - osqp
-- pandas 1.0.5 or later
-- scikit-learn 1.4 or 1.5
+- pandas 1.4.0 or later
+- scikit-learn 1.6
 - scipy
 - C/C++ compiler
 

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/README.rst

@@ -32,14 +32,14 @@ this unique characteristic of such a dataset into account.
 Requirements
 ============
 
-- Python 3.9 or later
+- Python 3.10 or later
 - ecos
 - joblib
 - numexpr
 - numpy
 - osqp
-- pandas 1.0.5 or later
-- scikit-learn 1.4 or 1.5
+- pandas 1.4.0 or later
+- scikit-learn 1.6
 - scipy
 - C/C++ compiler
 

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/api/datasets.rst

@@ -8,6 +8,8 @@ Datasets
     get_x_y
     load_aids
     load_arff_files_standardized
+    load_bmt
+    load_cgvhd
     load_breast_cancer
     load_flchain
     load_gbsg2

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/api/nonparametric.rst

@@ -7,6 +7,7 @@ Non-parametric Estimators
 
     CensoringDistributionEstimator
     SurvivalFunctionEstimator
+    cumulative_incidence_competing_risks
     ipc_weights
     kaplan_meier_estimator
     nelson_aalen_estimator

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/conf.py

@@ -217,7 +217,7 @@ extlinks = {
 }
 
 intersphinx_mapping = {
-    "sklearn": ("https://scikit-learn.org/1.5", None),
+    "sklearn": ("https://scikit-learn.org/1.6", None),
     "cython": ("https://cython.readthedocs.io/en/latest/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/contributing.rst

@@ -25,10 +25,10 @@ These are the steps you need to take to create a copy of the scikit-survival rep
 on your computer.
 
 
-1. `Create an account <https://github.com/join>`_ on
+1. `Create an account <https://github.com/signup>`_ on
    GitHub if you do not already have one.
 
-2. `Fork <https://help.github.com/en/github/getting-started-with-github/fork-a-repo>`_
+2. `Fork <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo>`_
    the `scikit-survival repository <https://github.com/sebp/scikit-survival>`_.
 
 3. Clone your fork of the scikit-survival repository from your GitHub account to your local disk.
@@ -130,7 +130,7 @@ Submitting a Pull Request
 
     git push -u origin my_feature
 
-4. `Create a pull request <https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request>`_.
+4. `Create a pull request <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request>`_.
 
 
 .. _building-documentation:
@@ -166,5 +166,5 @@ If you are new to Cython you may find the project's documentation on
 .. _Git: https://git-scm.com/
 .. _GitHub: https://github.com/sebp/scikit-survival
 .. _Sphinx: https://www.sphinx-doc.org/
-.. _tox: https://tox.readthedocs.io/en/latest/
+.. _tox: https://tox.wiki/en/stable/
 .. _pre-commit: https://pre-commit.com/#usage

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/index.rst

@@ -31,7 +31,7 @@ this unique characteristic of such a dataset into account.
         :link-type: doc
 
         The easiest way to install scikit-survival is to use
-        `Anaconda <https://www.anaconda.com/distribution/>`_ by running::
+        `conda-forge <https://conda-forge.org/download/>`_ by running::
 
           conda install -c conda-forge scikit-survival
 

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/install.rst

@@ -1,21 +1,30 @@
 Installing scikit-survival
 ==========================
 
-This is the recommended and easiest to install scikit-survival is to use
-:ref:`install-conda`.
+The recommended and easiest way to install scikit-survival is to use
+:ref:`install-conda` or :ref:`install-pip`.
+Pre-built binary packages for scikit-survival are available for Linux, macOS, and Windows.
 Alternatively, you can install scikit-survival :ref:`install-from-source`.
 
 .. _install-conda:
 
-Anaconda
---------
+conda
+-----
 
-Pre-built binary packages for Linux, MacOS, and Windows are available
-for `Anaconda <https://www.anaconda.com/distribution/>`_.
-If you have Anaconda installed, run::
+If you have `conda <https://docs.anaconda.com/>`_ installed, you can
+install scikit-survival from the ``conda-forge`` channel by running::
 
   conda install -c conda-forge scikit-survival
 
+.. _install-pip:
+
+pip
+---
+
+If you use ``pip``, install the latest release of scikit-survival with::
+
+  pip install scikit-survival
+
 
 .. _install-from-source:
 
@@ -31,9 +40,9 @@ On Linux, you need to install *gcc*, which in most cases is available
 via your distribution's packaging system.
 Please follow your distribution's instructions on how to install packages.
 
-**MacOS**
+**macOS**
 
-On MacOS, you need to install *clang*, which is available from
+On macOS, you need to install *clang*, which is available from
 the *Command Line Tools* package. Open a terminal and execute::
 
   xcode-select --install
@@ -55,7 +64,7 @@ Latest Release
 
 To install the latest release of scikit-survival from source, run::
 
-  pip install scikit-survival
+  pip install scikit-survival --no-binary scikit-survival
 
 
 .. note::
@@ -63,7 +72,7 @@ To install the latest release of scikit-survival from source, run::
     If you have not installed the :ref:`dependencies <dependencies>` previously, this command
     will first install all dependencies before installing scikit-survival.
     Therefore, installation might fail if build requirements of some dependencies
-    are not met. In particular, `osqp <https://github.com/oxfordcontrol/osqp-python>`_
+    are not met. In particular, `osqp <https://github.com/osqp/osqp-python>`_
     does require `CMake <https://cmake.org/>`_ to be installed.
 
 Development Version
@@ -84,13 +93,13 @@ Dependencies
 
 The current minimum dependencies to run scikit-survival are:
 
-- Python 3.9 or later
+- Python 3.10 or later
 - ecos
 - joblib
 - numexpr
 - numpy
 - osqp
-- pandas 1.0.5 or later
-- scikit-learn 1.4 or 1.5
+- pandas 1.4.0 or later
+- scikit-learn 1.6
 - scipy
 - C/C++ compiler

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/release_notes/v0.14.rst

@@ -45,5 +45,5 @@ Enhancements
 - Add :func:`sksurv.show_versions` that prints the version of all dependencies.
 - Add support for pandas 1.1
 - Include interactive notebooks in documentation on readthedocs.
-- Add user guide on `penalized Cox models <user_guide/coxnet.ipynb>`_.
-- Add user guide on `gradient boosted models <user_guide/boosting.ipynb>`_.
+- Add user guide on :ref:`penalized Cox models </user_guide/coxnet.ipynb>`.
+- Add user guide on :ref:`gradient boosted models </user_guide/boosting.ipynb>`.

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/release_notes/v0.23.rst

@@ -3,6 +3,28 @@
 What's new in 0.23
 ==================
 
+scikit-survival 0.23.1 (2024-11-04)
+-----------------------------------
+
+This release adds support for Python 3.13.
+The minimum required version for pandas has been bumped to pandas 1.4.0.
+
+Bug fixes
+^^^^^^^^^
+- Add `SurvivalAnalysisMixin` base class to :class:`sksurv.ensemble.ExtraSurvivalTrees`
+  to enable the :meth:`sksurv.ensemble.ExtraSurvivalTrees.score` method that has been
+  unintentionally removed in 0.23.0 (:issue:`488`).
+
+Enhancements
+^^^^^^^^^^^^
+- Improve performance of :func:`sksurv.metrics.concordance_index_censored` and
+  :func:`sksurv.metrics.concordance_index_ipcw` (:issue:`465`).
+
+Backwards incompatible changes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+- Support for pandas versions before 1.4.0 has been dropped.
+
+
 scikit-survival 0.23.0 (2024-06-30)
 -----------------------------------
 

scikit_survival-0.24.0/doc/release_notes/v0.24.rst

@@ -0,0 +1,46 @@
+.. _release_notes_0_24:
+
+What's new in 0.24
+==================
+
+scikit-survival 0.24.0 (2025-02-24)
+-----------------------------------
+
+This release adds support for scikit-learn 1.6, which includes missing-values support
+for :class:`sksurv.ensemble.ExtraSurvivalTrees`.
+Moreover, the release features :func:`sksurv.nonparametric.cumulative_incidence_competing_risks`
+which implements a non-parameteric estimator of the cumulative incidence function
+for competing risks.
+See the :ref:`user guide on the analysis of competing risks </user_guide/competing-risks.ipynb>`.
+
+Bug fixes
+^^^^^^^^^
+- In the C++ code of :class:`sksurv.linear_model.CoxnetSurvivalAnalysis`, set type of ``n_alphas``
+  to ``VectorType::Index`` instead of ``ìnt``, because on Windows,
+  int and Eigen's Index differ in size.
+- Fix printing of Python version in :func:`sksurv.show_versions`.
+- Give an error if ``max_sample`` is set, but ``bootstrap`` is False in
+  :class:`sksurv.ensemble.RandomSurvivalForest` and
+  :class:`sksurv.ensemble.ExtraSurvivalTrees`.
+
+Enhancements
+^^^^^^^^^^^^
+- Add :func:`sksurv.nonparametric.cumulative_incidence_competing_risks` to estimate
+  the cumulative incidence function in the case of competing risks (:issue:`491`, :issue:`500`).
+- Add :func:`sksurv.datasets.load_bmt` and :func:`sksurv.datasets.load_cgvhd` which are
+  datasets with competing risks (:issue:`491`, :issue:`500`).
+- Add missing-values support to :class:`sksurv.ensemble.ExtraSurvivalTrees` (:issue:`504`).
+- Add ``estimators_samples_`` property to :class:`sksurv.ensemble.RandomSurvivalForest` and
+  :class:`sksurv.ensemble.ExtraSurvivalTrees`.
+- Upgrade syntax to Python 3.10.
+- Run nbval with Python 3.12, matplotlib 3.9, and seaborn 0.13.
+
+Documentation
+^^^^^^^^^^^^^
+- Fix links in documentation.
+- Add :ref:`user guide on the analysis of competing risks </user_guide/competing-risks.ipynb>`.
+
+Backwards incompatible changes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+- Support for scikit-learn versions before 1.6.1 has been dropped (:issue:`504`).
+- Support for Python versions before 3.10 has been dropped.

{scikit_survival-0.23.0 → scikit_survival-0.24.0}/doc/release_notes.rst

@@ -4,6 +4,7 @@ Release Notes
 .. toctree::
   :maxdepth: 2
 
+  release_notes/v0.24
   release_notes/v0.23
   release_notes/v0.22
   release_notes/v0.21