scikit-survival 0.19.0__tar.gz → 0.20.0__tar.gz

{scikit-survival-0.19.0/scikit_survival.egg-info → scikit-survival-0.20.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-survival
-Version: 0.19.0
+Version: 0.20.0
 Summary: Survival analysis built on top of scikit-learn
 Home-page: https://github.com/sebp/scikit-survival
 Author: Sebastian Pölsterl
@@ -30,7 +30,7 @@ License-File: COPYING
 
 |License| |Docs| |DOI|
 
-|build-linux| |build-macos| |build-windows| |Codecov| |Codacy|
+|build-tests| |build-windows| |Codecov| |Codacy|
 
 ***************
 scikit-survival
@@ -69,7 +69,7 @@ Requirements
 - numpy 1.17.3 or later
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.1
+- scikit-learn 1.2
 - scipy 1.3.2 or later
 - C/C++ compiler
 
@@ -164,13 +164,9 @@ Please cite the following paper if you are using **scikit-survival**.
    :target: https://zenodo.org/badge/latestdoi/77409504
    :alt: Digital Object Identifier (DOI)
 
-.. |build-linux| image:: https://github.com/sebp/scikit-survival/workflows/Linux/badge.svg?branch=master
-  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3ALinux+branch%3Amaster+
-  :alt: Linux Build Status
-
-.. |build-macos| image:: https://github.com/sebp/scikit-survival/workflows/macOS/badge.svg?branch=master
-  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3AmacOS+branch%3Amaster+
-  :alt: macOS Build Status
+.. |build-tests| image:: https://github.com/sebp/scikit-survival/actions/workflows/tests-workflow.yaml/badge.svg?branch=master
+  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3Atests+branch%3Amaster
+  :alt: GitHub Actions Tests Status
 
 .. |build-windows| image:: https://ci.appveyor.com/api/projects/status/github/sebp/scikit-survival?branch=master&svg=true
    :target: https://ci.appveyor.com/project/sebp/scikit-survival

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/README.rst

@@ -1,6 +1,6 @@
 |License| |Docs| |DOI|
 
-|build-linux| |build-macos| |build-windows| |Codecov| |Codacy|
+|build-tests| |build-windows| |Codecov| |Codacy|
 
 ***************
 scikit-survival
@@ -39,7 +39,7 @@ Requirements
 - numpy 1.17.3 or later
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.1
+- scikit-learn 1.2
 - scipy 1.3.2 or later
 - C/C++ compiler
 
@@ -134,13 +134,9 @@ Please cite the following paper if you are using **scikit-survival**.
    :target: https://zenodo.org/badge/latestdoi/77409504
    :alt: Digital Object Identifier (DOI)
 
-.. |build-linux| image:: https://github.com/sebp/scikit-survival/workflows/Linux/badge.svg?branch=master
-  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3ALinux+branch%3Amaster+
-  :alt: Linux Build Status
-
-.. |build-macos| image:: https://github.com/sebp/scikit-survival/workflows/macOS/badge.svg?branch=master
-  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3AmacOS+branch%3Amaster+
-  :alt: macOS Build Status
+.. |build-tests| image:: https://github.com/sebp/scikit-survival/actions/workflows/tests-workflow.yaml/badge.svg?branch=master
+  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3Atests+branch%3Amaster
+  :alt: GitHub Actions Tests Status
 
 .. |build-windows| image:: https://ci.appveyor.com/api/projects/status/github/sebp/scikit-survival?branch=master&svg=true
    :target: https://ci.appveyor.com/project/sebp/scikit-survival

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/doc/conf.py

@@ -49,12 +49,16 @@ extensions = [
     'sphinx.ext.autosummary',
     'sphinx.ext.coverage',
     'sphinx.ext.extlinks',
+    'sphinx.ext.intersphinx',
     'sphinx.ext.linkcode',
     'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
+    'sphinxcontrib.spelling',
     'nbsphinx',
 ]
 
+spelling_word_list_filename = 'spelling_wordlist.txt'
+
 autosummary_generate = True
 autodoc_default_options = {
     'members': None,
@@ -199,6 +203,7 @@ extlinks = {
     'issue': ('https://github.com/sebp/scikit-survival/issues/%s', '#'),
 }
 
+intersphinx_mapping = {'sklearn': ('https://scikit-learn.org/1.2', None)}
 
 def linkcode_resolve(domain, info):
     """

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/doc/docs_requirements.txt

@@ -1,8 +1,9 @@
 # This file purposely does not contain libraries that depend on C modules.
 # See https://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
-ipython
+ipython !=8.7.0
 nbsphinx
 docutils
 setuptools_scm
 sphinx ~=4.4.0
 pydata-sphinx-theme ~=0.8.1
+sphinxcontrib-spelling

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/doc/install.rst

@@ -91,6 +91,6 @@ The current minimum dependencies to run scikit-survival are:
 - numpy 1.17.3 or later
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.1
+- scikit-learn 1.2
 - scipy 1.3.2 or later
 - C/C++ compiler

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/doc/release_notes.rst

@@ -1,6 +1,33 @@
 Release Notes
 =============
 
+scikit-survival 0.20.0 (2023-03-05)
+-----------------------------------
+
+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
+  `sklearn#23462 <https://github.com/scikit-learn/scikit-learn/issues/23462>`_).
+- Add ``positive`` and ``random_state`` parameters to :class:`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 :class:`sksurv.linear_model.IPCRidge`.
+- Remove deprecated ``X_idx_sorted`` argument from :meth:`sksurv.tree.SurvivalTree.fit`.
+- Setting ``kernel="polynomial"`` in :class:`sksurv.svm.FastKernelSurvivalSVM`,
+  :class:`sksurv.svm.HingeLossSurvivalSVM`, and :class:`sksurv.svm.MinlipSurvivalAnalysis`
+  has been replaced with ``kernel="poly"``.
+
+
 scikit-survival 0.19.0 (2022-10-23)
 -----------------------------------
 
@@ -110,7 +137,7 @@ Enhancements
 - Add support for ``feature_names_in_`` and ``n_features_in_``
   to all estimators and transforms.
 - Add :meth:`sksurv.preprocessing.OneHotEncoder.get_feature_names_out`.
-- Update bundeled version of Eigen to 3.3.9.
+- Update bundled version of Eigen to 3.3.9.
 
 Backwards incompatible changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -124,7 +151,7 @@ Deprecations
 ^^^^^^^^^^^^
 - The ``normalize`` parameter of :class:`sksurv.linear_model.IPCRidge`
   is deprecated and will be removed in a future version. Instead, use
-  a sciki-learn pipeline:
+  a scikit-learn pipeline:
   ``make_pipeline(StandardScaler(with_mean=False), IPCRidge())``.
 
 
@@ -370,9 +397,9 @@ Bug fixes
   - :func:`sksurv.metrics.cumulative_dynamic_auc`
   - :func:`sksurv.metrics.concordance_index_ipcw`
 
-- Throw an exception when trying to estimate c-index from uncomparable data (#117).
+- Throw an exception when trying to estimate c-index from incomparable data (#117).
 - Estimators in ``sksurv.svm`` will now throw an
-  exception when trying to fit a model to data with uncomparable pairs.
+  exception when trying to fit a model to data with incomparable pairs.
 
 
 scikit-survival 0.12 (2020-04-15)

scikit-survival-0.20.0/doc/spelling_wordlist.txt

@@ -0,0 +1,55 @@
+arff
+biomarker
+Breiman
+Breslow
+boolean
+callables
+Covariance
+covariance
+covariates
+cvxpy
+cvxopt
+Cython
+DataFrame
+dataframe
+dataset
+datasets
+Deprecations
+dimensionality
+discriminative
+dtype
+dtypes
+Efron
+Eigen
+filename
+hyperplane
+infeasible
+Kaplan-Meier
+Lipschitz
+macOS
+mae
+mse
+ndarray
+Nelson-Aalen
+numpy
+overfitting
+params
+parameterized
+precomputed
+Pre-Processing
+reStructuredText
+readthedocs
+scikit
+scikit-learn
+scikit-survival
+scipy
+sigmoid
+sklearn
+sksurv
+sqrt
+stagewise
+subobjects
+subsampling
+tol
+Uno
+unpenalized

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/doc/user_guide/evaluating-survival-models.ipynb

@@ -1088,7 +1088,7 @@
     "While [as_concordance_index_ipcw_scorer](https://scikit-survival.readthedocs.io/en/latest/api/generated/sksurv.metrics.as_concordance_index_ipcw_scorer.html#sksurv.metrics.as_concordance_index_ipcw_scorer)\n",
     "and [as_cumulative_dynamic_auc_scorer](https://scikit-survival.readthedocs.io/en/latest/api/generated/sksurv.metrics.as_cumulative_dynamic_auc_scorer.html#sksurv.metrics.as_cumulative_dynamic_auc_scorer)\n",
     "can be used with any estimator,\n",
-    "[as_integrated_brier_score_scorer](https://scikit-survival.readthedocs.io/en/latest/api/generated/sksurv.metrics.as_integrated_brier_score_scorer.html#sksurv.metrics.as_integrated_brier_score_scorer) is only available for estimators that provide the ``predict_survival_function`` method, which includes ``RandomSurvivalForest``. If available, hyper-parameters that maximize the **negative** intergrated time-dependent Brier score will be selected, because a lower Brier score indicates better performance."
+    "[as_integrated_brier_score_scorer](https://scikit-survival.readthedocs.io/en/latest/api/generated/sksurv.metrics.as_integrated_brier_score_scorer.html#sksurv.metrics.as_integrated_brier_score_scorer) is only available for estimators that provide the ``predict_survival_function`` method, which includes ``RandomSurvivalForest``. If available, hyper-parameters that maximize the **negative** integrated time-dependent Brier score will be selected, because a lower Brier score indicates better performance."
    ]
   },
   {

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/pyproject.toml

@@ -18,8 +18,8 @@ requires = [
     "numpy; python_version>'3.10'",
 
     # scikit-learn requirements
-    "scikit-learn~=1.1.0; python_version<='3.9'",
-    "scikit-learn~=1.1.0; python_version=='3.10'",
+    "scikit-learn~=1.2.0; python_version<='3.9'",
+    "scikit-learn~=1.2.0; python_version=='3.10'",
     "scikit-learn; python_version>'3.10'",
 ]
 build-backend = "setuptools.build_meta"

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/requirements/prod.txt

@@ -5,4 +5,4 @@ numpy
 osqp !=0.6.0,!=0.6.1
 pandas >=1.0.5
 scipy >=1.3.2
-scikit-learn >=1.1.0,<1.2
+scikit-learn >=1.2.0,<1.3

{scikit-survival-0.19.0 → scikit-survival-0.20.0/scikit_survival.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-survival
-Version: 0.19.0
+Version: 0.20.0
 Summary: Survival analysis built on top of scikit-learn
 Home-page: https://github.com/sebp/scikit-survival
 Author: Sebastian Pölsterl
@@ -30,7 +30,7 @@ License-File: COPYING
 
 |License| |Docs| |DOI|
 
-|build-linux| |build-macos| |build-windows| |Codecov| |Codacy|
+|build-tests| |build-windows| |Codecov| |Codacy|
 
 ***************
 scikit-survival
@@ -69,7 +69,7 @@ Requirements
 - numpy 1.17.3 or later
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.1
+- scikit-learn 1.2
 - scipy 1.3.2 or later
 - C/C++ compiler
 
@@ -164,13 +164,9 @@ Please cite the following paper if you are using **scikit-survival**.
    :target: https://zenodo.org/badge/latestdoi/77409504
    :alt: Digital Object Identifier (DOI)
 
-.. |build-linux| image:: https://github.com/sebp/scikit-survival/workflows/Linux/badge.svg?branch=master
-  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3ALinux+branch%3Amaster+
-  :alt: Linux Build Status
-
-.. |build-macos| image:: https://github.com/sebp/scikit-survival/workflows/macOS/badge.svg?branch=master
-  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3AmacOS+branch%3Amaster+
-  :alt: macOS Build Status
+.. |build-tests| image:: https://github.com/sebp/scikit-survival/actions/workflows/tests-workflow.yaml/badge.svg?branch=master
+  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3Atests+branch%3Amaster
+  :alt: GitHub Actions Tests Status
 
 .. |build-windows| image:: https://ci.appveyor.com/api/projects/status/github/sebp/scikit-survival?branch=master&svg=true
    :target: https://ci.appveyor.com/project/sebp/scikit-survival

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/scikit_survival.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ doc/docs_requirements.txt
 doc/index.rst
 doc/install.rst
 doc/release_notes.rst
+doc/spelling_wordlist.txt
 doc/_static/buttons.js
 doc/_static/custom.css
 doc/_static/images/censoring.svg

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/scikit_survival.egg-info/requires.txt

@@ -5,4 +5,4 @@ numpy
 osqp!=0.6.0,!=0.6.1
 pandas>=1.0.5
 scipy>=1.3.2
-scikit-learn<1.2,>=1.1.0
+scikit-learn<1.3,>=1.2.0

{scikit-survival-0.19.0 → scikit-survival-0.20.0}/sksurv/datasets/base.py

@@ -410,7 +410,7 @@ def load_flchain():
 
     .. [2] Dispenzieri, A., Katzmann, J., Kyle, R., Larson, D., Therneau, T., Colby, C., Clark, R.,
            Mead, G., Kumar, S., Melton III, LJ. and Rajkumar, SV.
-           Use of monclonal serum immunoglobulin free light chains to predict overall survival in
+           Use of nonclonal serum immunoglobulin free light chains to predict overall survival in
            the general population, Mayo Clinic Proceedings 87:512-523. (2012)
     """
     fn = resource_filename(__name__, 'data/flchain.arff')