scikit-survival 0.22.1__tar.gz → 0.23.0__tar.gz

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/MANIFEST.in

@@ -6,7 +6,7 @@ prune doc/api/generated
 prune .binder
 prune .github
 prune ci
-exclude appveyor.yml .codecov.yml .readthedocs.yaml .zenodo.json
+exclude appveyor.yml .codecov.yml .pre-commit-config.yaml .readthedocs.yaml .zenodo.json
 
 global-exclude __pycache__
 global-exclude .ipynb_checkpoints

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-survival
-Version: 0.22.1
+Version: 0.23.0
 Summary: Survival analysis built on top of scikit-learn
 Author-email: Sebastian Pölsterl <sebp@k-d-w.org>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -694,34 +694,33 @@ Classifier: Programming Language :: C++
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 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: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: COPYING
 Requires-Dist: ecos
-Requires-Dist: importlib-resources>=1.3; python_version < "3.9"
 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: scipy>=1.3.2
-Requires-Dist: scikit-learn<1.4,>=1.3.0
+Requires-Dist: scikit-learn<1.6,>=1.4.0
 Provides-Extra: dev
 Requires-Dist: black[jupyter]; extra == "dev"
 Requires-Dist: build; extra == "dev"
 Requires-Dist: coverage; extra == "dev"
-Requires-Dist: cython>=0.29; extra == "dev"
+Requires-Dist: Cython>=3.0.10; extra == "dev"
 Requires-Dist: packaging; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
-Requires-Dist: setuptools-scm>=6.4; extra == "dev"
+Requires-Dist: setuptools-scm>=8; extra == "dev"
 Requires-Dist: tomli; extra == "dev"
 Requires-Dist: tox; extra == "dev"
 Provides-Extra: docs
@@ -729,10 +728,10 @@ Requires-Dist: ipython!=8.7.0; extra == "docs"
 Requires-Dist: nbsphinx>=0.9.2; extra == "docs"
 Requires-Dist: docutils; extra == "docs"
 Requires-Dist: setuptools-scm; extra == "docs"
-Requires-Dist: sphinx~=6.2.1; extra == "docs"
-Requires-Dist: pydata-sphinx-theme~=0.13.3; extra == "docs"
+Requires-Dist: sphinx~=7.3.7; extra == "docs"
+Requires-Dist: pydata-sphinx-theme~=0.15.2; extra == "docs"
 Requires-Dist: sphinxcontrib-spelling; extra == "docs"
-Requires-Dist: sphinx-design~=0.4.1; extra == "docs"
+Requires-Dist: sphinx-design~=0.5.0; extra == "docs"
 Requires-Dist: sphinx-copybutton~=0.5.2; extra == "docs"
 Provides-Extra: nbval
 Requires-Dist: ipykernel; extra == "nbval"
@@ -776,15 +775,15 @@ this unique characteristic of such a dataset into account.
 Requirements
 ============
 
-- Python 3.8 or later
+- Python 3.9 or later
 - ecos
 - joblib
 - numexpr
-- numpy 1.17.3 or later
+- numpy
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.3
-- scipy 1.3.2 or later
+- scikit-learn 1.4 or 1.5
+- scipy
 - C/C++ compiler
 
 ============
@@ -794,7 +793,7 @@ Installation
 The easiest way to install scikit-survival is to use
 `Anaconda <https://www.anaconda.com/distribution/>`_ by running::
 
-  conda install -c sebp scikit-survival
+  conda install -c conda-forge scikit-survival
 
 Alternatively, you can install scikit-survival from source
 following `this guide <https://scikit-survival.readthedocs.io/en/stable/install.html#from-source>`_.
@@ -867,7 +866,7 @@ Please cite the following paper if you are using **scikit-survival**.
   :alt: codecov
 
 .. |Codacy| image:: https://api.codacy.com/project/badge/Grade/17242004cdf6422c9a1052bf1ec63104
-   :target: https://www.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=sebp/scikit-survival&amp;utm_campaign=Badge_Grade
+   :target: https://app.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
    :alt: Codacy Badge
 
 .. |Docs| image:: https://readthedocs.org/projects/scikit-survival/badge/?version=latest

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/README.rst

@@ -32,15 +32,15 @@ this unique characteristic of such a dataset into account.
 Requirements
 ============
 
-- Python 3.8 or later
+- Python 3.9 or later
 - ecos
 - joblib
 - numexpr
-- numpy 1.17.3 or later
+- numpy
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.3
-- scipy 1.3.2 or later
+- scikit-learn 1.4 or 1.5
+- scipy
 - C/C++ compiler
 
 ============
@@ -50,7 +50,7 @@ Installation
 The easiest way to install scikit-survival is to use
 `Anaconda <https://www.anaconda.com/distribution/>`_ by running::
 
-  conda install -c sebp scikit-survival
+  conda install -c conda-forge scikit-survival
 
 Alternatively, you can install scikit-survival from source
 following `this guide <https://scikit-survival.readthedocs.io/en/stable/install.html#from-source>`_.
@@ -123,7 +123,7 @@ Please cite the following paper if you are using **scikit-survival**.
   :alt: codecov
 
 .. |Codacy| image:: https://api.codacy.com/project/badge/Grade/17242004cdf6422c9a1052bf1ec63104
-   :target: https://www.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=sebp/scikit-survival&amp;utm_campaign=Badge_Grade
+   :target: https://app.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
    :alt: Codacy Badge
 
 .. |Docs| image:: https://readthedocs.org/projects/scikit-survival/badge/?version=latest

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/doc/_static/custom.css

@@ -23,7 +23,7 @@ table {
     font-weight: var(--pst-font-weight-heading) !important;
 }
 
-.overview-grid .sd-card-title .fas {
+.overview-grid .sd-card-title svg[data-prefix="fas"] {
     position: absolute;
     right: 1.2rem;
     line-height: 1.4;
@@ -55,38 +55,68 @@ table {
     opacity: 1;
 }
 
-.github-icon, .github-repository {
+.github-icon {
     display: inline-block;
+    vertical-align: middle;
 }
 
-.github-icon {
-    width: 1.8rem;
+.github-icon span {
+    padding: .5rem;
 }
 
-.github-icon i {
-    font-size: calc(var(--pst-font-size-icon) - .1rem);
+.github-repository-name {
+    display: inline-block;
+    max-width: calc(100% - 1.2rem);
+    overflow: hidden;
+    text-overflow: ellipsis;
+    vertical-align: middle;
 }
 
 .navbar-icon-links ul.github-facts {
-    margin: 0;
+    display: flex;
+    gap: .4rem;
+    margin: .1rem 0 0;
     padding: 0;
     font-size: .95rem;
-    font-weight: 700;
+    font-weight: 400;
     list-style: none;
     opacity: .75;
     overflow: hidden;
     text-overflow: ellipsis;
+    width: 100%;
 }
 
-.navbar-icon-links .github-fact {
+li.github-fact {
     display: inline-block;
+    vertical-align: middle;
+}
+
+.github-fact-stars::before {
+    font: var(--fa-font-solid);
+    content: '\f005';
+    margin-right: .15rem;
 }
 
-.navbar-icon-links .github-fact::before {
-    margin: 0.2rem;
-    content: "\00B7"
+.github-fact-forks::before {
+    font: var(--fa-font-solid);
+    content: '\e13b';
+    margin-right: .15rem;
 }
 
-.navbar-icon-links .github-fact:first-child::before {
-    display: none
+a:hover.github-repository {
+    text-decoration: none;
+    color: var(--pst-color-link-hover);
+}
+
+a.github-repository {
+    color: var(--pst-color-text-muted);
+}
+
+a:visited.github-repository {
+    color: var(--pst-color-text-muted);
+}
+
+a:visited:hover.github-repository  {
+    text-decoration: none;
+    color: var(--pst-color-link-hover);
 }

scikit_survival-0.23.0/doc/_static/github-stats.js

@@ -0,0 +1,69 @@
+"use strict";
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+function round(value) {
+    if (value > 999) {
+        let digits = +((value - 950) % 1000 > 99);
+        return `${((value + 0.000001) / 1000).toFixed(digits)}k`;
+    }
+    else {
+        return value.toString();
+    }
+}
+function get_stats(repo) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const response = yield fetch("https://api.github.com/repos" + repo, {
+            headers: {
+                "Accept": "application/vnd.github+json",
+                "X-GitHub-Api-Version": "2022-11-28",
+            },
+            redirect: "follow",
+        });
+        return response.json();
+    });
+}
+function get_repo_url() {
+    const repoElem = document.querySelector("a.github-repository");
+    if (repoElem == null) {
+        return null;
+    }
+    const url_str = repoElem.getAttribute("href");
+    if (url_str != null) {
+        return new URL(url_str);
+    }
+    return null;
+}
+function append_element_stats(elements, text, css_class) {
+    elements.forEach((elem) => {
+        let child = document.createElement("li");
+        child.setAttribute("class", `github-fact ${css_class}`);
+        const txt = document.createTextNode(text);
+        child.appendChild(txt);
+        elem.appendChild(child);
+    });
+}
+function update_repo_stats() {
+    const url = get_repo_url();
+    if (url == null)
+        return;
+    let stats_elem = document.querySelectorAll("ul.github-facts");
+    get_stats(url.pathname).then((data) => {
+        append_element_stats(stats_elem, round(data["stargazers_count"]), "github-fact-stars");
+        append_element_stats(stats_elem, round(data["forks_count"]), "github-fact-forks");
+    });
+}
+function update_repo_stats_once() {
+    return __awaiter(this, void 0, void 0, function* () {
+        document.removeEventListener("DOMContentLoaded", update_repo_stats);
+        update_repo_stats();
+    });
+}
+document.addEventListener("DOMContentLoaded", update_repo_stats_once);
+//# sourceMappingURL=github-stats.js.map

scikit_survival-0.23.0/doc/_templates/navbar-github-links.html

@@ -0,0 +1,12 @@
+<div class="navbar-icon-links navbar-nav"
+    aria-label="{{ theme_icon_links_label }}">
+  <a class="nav-link github-repository" href="https://github.com/sebp/scikit-survival" rel="noopener" target="_blank" title="Go to repository">
+    <div class="github-icon">
+      <span><i class="fa-brands fa-github fa-lg"></i></span>
+    </div>
+    <div class="github-repository-name">
+      {{ project }}
+      <ul class="github-facts"></ul>
+    </div>
+  </a>
+</div>

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/doc/conf.py

@@ -12,7 +12,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from datetime import datetime
+from datetime import datetime, UTC
 from importlib.metadata import version as get_version
 import inspect
 import os
@@ -85,7 +85,7 @@ master_doc = "index"
 
 # General information about the project.
 project = "scikit-survival"
-current_year = datetime.utcnow().year
+current_year = datetime.now(UTC).year
 copyright = f"2015-{current_year}, Sebastian Pölsterl and contributors"
 
 # The version info for the project you're documenting, acts as replacement for
@@ -175,6 +175,14 @@ html_theme_options = {
     "secondary_sidebar_items": ["page-toc"],
     "navbar_end": ["theme-switcher.html", "navbar-github-links.html"],
     "navbar_persistent": ["search-field.html"],
+    "navbar_align": "left",
+    "navigation_with_keys": False,
+}
+
+html_sidebars = {
+    "cite": [],
+    "contributing": [],
+    "install": [],
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -197,7 +205,7 @@ html_title = f"scikit-survival {version}"
 # html_favicon = None
 
 html_css_files = ["custom.css"]
-html_js_files = ["buttons.js"]
+html_js_files = ["github-stats.js"]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -208,7 +216,12 @@ extlinks = {
     "issue": ("https://github.com/sebp/scikit-survival/issues/%s", "#%s"),
 }
 
-intersphinx_mapping = {"sklearn": ("https://scikit-learn.org/1.3", None)}
+intersphinx_mapping = {
+    "sklearn": ("https://scikit-learn.org/1.5", None),
+    "cython": ("https://cython.readthedocs.io/en/latest/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+}
 
 
 def linkcode_resolve(domain, info):

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/doc/contributing.rst

@@ -1,3 +1,5 @@
+.. _contributing:
+
 Contributing Guidelines
 =======================
 
@@ -13,7 +15,10 @@ scikit-survival is developed on `GitHub`_ using the `Git`_ version control syste
 The preferred way to contribute to scikit-survival is to fork
 the main repository on GitHub, then submit a *pull request* (PR).
 
-Creating a fork
+
+.. _forking:
+
+Creating a Fork
 ---------------
 
 These are the steps you need to take to create a copy of the scikit-survival repository
@@ -33,6 +38,8 @@ on your computer.
     cd scikit-survival
 
 
+.. _setup-dev-environment:
+
 Setting up a Development Environment
 ------------------------------------
 
@@ -58,6 +65,9 @@ These are the steps you need to take.
 
     pip install -e .[dev]
 
+
+.. _making-changes-to-code:
+
 Making Changes to the Code
 --------------------------
 For a pull request to be accepted, your changes must meet the below requirements.
@@ -97,6 +107,9 @@ For a pull request to be accepted, your changes must meet the below requirements
    is compatible and include the license information in the contributed files,
    or obtain a permission from the original author to relicense the contributed code.
 
+
+.. _submit-pull-request:
+
 Submitting a Pull Request
 -------------------------
 
@@ -120,6 +133,8 @@ Submitting a Pull Request
 4. `Create a pull request <https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request>`_.
 
 
+.. _building-documentation:
+
 Building the Documentation
 --------------------------
 
@@ -134,7 +149,20 @@ of the documentation, run::
 
   xdg-open _build/html/index.html
 
+
+.. _building-cython-code:
+
+Building Cython Code
+--------------------
+
+Part of the code base is written in `Cython`_. To rebuild this code after making changes,
+please re-run the install command from the :ref:`setup-dev-environment` section.
+
+If you are new to Cython you may find the project's documentation on
+:ref:`debugging <cython:debugging>` and :ref:`profiling <cython:profiling>` helpful.
+
 .. _conda: https://conda.io/miniconda.html
+.. _Cython: https://cython.org
 .. _Git: https://git-scm.com/
 .. _GitHub: https://github.com/sebp/scikit-survival
 .. _Sphinx: https://www.sphinx-doc.org/

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/doc/index.rst

@@ -33,7 +33,7 @@ this unique characteristic of such a dataset into account.
         The easiest way to install scikit-survival is to use
         `Anaconda <https://www.anaconda.com/distribution/>`_ by running::
 
-          conda install -c sebp scikit-survival
+          conda install -c conda-forge scikit-survival
 
         Alternatively, you can install scikit-survival from source
         following :ref:`this guide <install-from-source>`.

{scikit-survival-0.22.1 → scikit_survival-0.23.0}/doc/install.rst

@@ -14,7 +14,7 @@ Pre-built binary packages for Linux, MacOS, and Windows are available
 for `Anaconda <https://www.anaconda.com/distribution/>`_.
 If you have Anaconda installed, run::
 
-  conda install -c sebp scikit-survival
+  conda install -c conda-forge scikit-survival
 
 
 .. _install-from-source:
@@ -84,13 +84,13 @@ Dependencies
 
 The current minimum dependencies to run scikit-survival are:
 
-- Python 3.8 or later
+- Python 3.9 or later
 - ecos
 - joblib
 - numexpr
-- numpy 1.17.3 or later
+- numpy
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.3
-- scipy 1.3.2 or later
+- scikit-learn 1.4 or 1.5
+- scipy
 - C/C++ compiler

scikit_survival-0.23.0/doc/release_notes/v0.1.rst

@@ -0,0 +1,11 @@
+.. _release_notes_0_1:
+
+What's new in 0.1
+=================
+
+scikit-survival 0.1 (2016-12-29)
+--------------------------------
+
+This is the initial release of scikit-survival.
+It combines the `implementation of survival support vector machines <https://github.com/tum-camp/survival-support-vector-machine>`_
+with the code used in the `Prostate Cancer DREAM challenge <https://f1000research.com/articles/5-2676/>`_.

scikit_survival-0.23.0/doc/release_notes/v0.10.rst

@@ -0,0 +1,27 @@
+.. _release_notes_0_10:
+
+What's new in 0.10
+==================
+
+scikit-survival 0.10 (2019-09-02)
+---------------------------------
+
+This release adds the `ties` argument to :class:`sksurv.linear_model.CoxPHSurvivalAnalysis`
+to choose between Breslow's and Efron's likelihood in the presence of tied event times.
+Moreover, :func:`sksurv.compare.compare_survival` has been added, which implements
+the log-rank hypothesis test for comparing the survival function of 2 or more groups.
+
+Enhancements
+^^^^^^^^^^^^
+
+- Update API doc of predict function of boosting estimators (#75).
+- Clarify documentation for GradientBoostingSurvivalAnalysis (#78).
+- Implement Efron's likelihood for handling tied event times.
+- Implement log-rank test for comparing survival curves.
+- Add support for scipy 1.3.1 (#66).
+
+Bug fixes
+^^^^^^^^^
+
+- Re-add `baseline_survival_` and `cum_baseline_hazard_` attributes
+  to :class:`sksurv.linear_model.CoxPHSurvivalAnalysis` (#76).

scikit_survival-0.23.0/doc/release_notes/v0.11.rst

@@ -0,0 +1,38 @@
+.. _release_notes_0_11:
+
+What's new in 0.11
+==================
+
+scikit-survival 0.11 (2019-12-21)
+---------------------------------
+
+This release adds :class:`sksurv.tree.SurvivalTree` and :class:`sksurv.ensemble.RandomSurvivalForest`,
+which are based on the log-rank split criterion.
+It also adds the OSQP solver as option to :class:`sksurv.svm.MinlipSurvivalAnalysis`
+and :class:`sksurv.svm.HingeLossSurvivalSVM`, which will replace the now deprecated
+`cvxpy` and `cvxopt` options in a future release.
+
+This release removes support for sklearn 0.20 and requires sklearn 0.21.
+
+Deprecations
+^^^^^^^^^^^^
+
+- The `cvxpy` and `cvxopt` options for `solver` in :class:`sksurv.svm.MinlipSurvivalAnalysis`
+  and :class:`sksurv.svm.HingeLossSurvivalSVM` are deprecated and will be removed in a future
+  version. Choosing `osqp` is the preferred option now.
+
+Enhancements
+^^^^^^^^^^^^
+
+- Add support for pandas 0.25.
+- Add OSQP solver option to :class:`sksurv.svm.MinlipSurvivalAnalysis` and
+  :class:`sksurv.svm.HingeLossSurvivalSVM` which has no additional dependencies.
+- Fix issue when using cvxpy 1.0.16 or later.
+- Explicitly specify utf-8 encoding when reading README.rst (#89).
+- Add :class:`sksurv.tree.SurvivalTree` and :class:`sksurv.ensemble.RandomSurvivalForest` (#90).
+
+Bug fixes
+^^^^^^^^^
+
+- Exclude Cython-generated files from source distribution because
+  they are not forward compatible.

scikit_survival-0.23.0/doc/release_notes/v0.12.rst

@@ -0,0 +1,39 @@
+.. _release_notes_0_12:
+
+What's new in 0.12
+==================
+
+scikit-survival 0.12 (2020-04-15)
+---------------------------------
+
+This release adds support for scikit-learn 0.22, thereby dropping support for
+older versions. Moreover, the regularization strength of the ridge penalty
+in :class:`sksurv.linear_model.CoxPHSurvivalAnalysis` can now be set per
+feature. If you want one or more features to enter the model unpenalized,
+set the corresponding penalty weights to zero.
+Finally, :class:`sklearn.pipeline.Pipeline` will now be automatically patched
+to add support for `predict_cumulative_hazard_function` and `predict_survival_function`
+if the underlying estimator supports it.
+
+Deprecations
+^^^^^^^^^^^^
+
+- Add scikit-learn's deprecation of `presort` in :class:`sksurv.tree.SurvivalTree` and
+  :class:`sksurv.ensemble.GradientBoostingSurvivalAnalysis`.
+- Add warning that default `alpha_min_ratio` in :class:`sksurv.linear_model.CoxnetSurvivalAnalysis`
+  will depend on the ratio of the number of samples to the number of features
+  in the future (#41).
+
+Enhancements
+^^^^^^^^^^^^
+
+- Add references to API doc of :class:`sksurv.ensemble.GradientBoostingSurvivalAnalysis` (#91).
+- Add support for pandas 1.0 (#100).
+- Add `ccp_alpha` parameter for
+  `Minimal Cost-Complexity Pruning <https://scikit-learn.org/stable/modules/tree.html#minimal-cost-complexity-pruning>`_
+  to :class:`sksurv.ensemble.GradientBoostingSurvivalAnalysis`.
+- Patch :class:`sklearn.pipeline.Pipeline` to add support for
+  `predict_cumulative_hazard_function` and `predict_survival_function`
+  if the underlying estimator supports it.
+- Allow per-feature regularization for :class:`sksurv.linear_model.CoxPHSurvivalAnalysis` (#102).
+- Clarify API docs of :func:`sksurv.metrics.concordance_index_censored` (#96).