Raise minimum required Python version to 3.10

.github/workflows/tests-workflow.yaml

@@ -12,7 +12,6 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - py39
           - py310
           - py311
           - py312

.github/workflows/wheels-workflow.yaml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-22.04, windows-2019, macos-13, macos-14]
-        python: [39, 310, 311, 312, 313]
+        python: [310, 311, 312, 313]
 
     steps:
       - uses: actions/checkout@v4

README.rst

@@ -32,7 +32,7 @@ this unique characteristic of such a dataset into account.
 Requirements
 ============
 
-- Python 3.9 or later
+- Python 3.10 or later
 - ecos
 - joblib
 - numexpr

appveyor.yml

@@ -5,8 +5,6 @@ image: Visual Studio 2019
 environment:
   # see https://www.appveyor.com/docs/build-environment/#python
   matrix:
-    - TARGET_ARCH: "x64"
-      CONDA_PY: "39"
     - TARGET_ARCH: "x64"
       CONDA_PY: "310"
     - TARGET_ARCH: "x64"

doc/install.rst

@@ -93,7 +93,7 @@ Dependencies
 
 The current minimum dependencies to run scikit-survival are:
 
-- Python 3.9 or later
+- Python 3.10 or later
 - ecos
 - joblib
 - numexpr

pyproject.toml

@@ -23,7 +23,7 @@ authors = [
     {name = "Sebastian Pölsterl", email = "sebp@k-d-w.org"}
 ]
 license = {file = "COPYING"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
@@ -36,10 +36,10 @@ classifiers = [
     "Programming Language :: Cython",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Software Development",
     "Topic :: Scientific/Engineering"
 ]
@@ -113,7 +113,7 @@ namespaces = false
 [tool.black]
 line-length = 120
 extend-exclude = "sksurv/linear_model/src/eigen"
-target-version = ["py39"]
+target-version = ["py310"]
 
 [tool.pytest.ini_options]
 minversion = "6.0"
@@ -182,7 +182,7 @@ extend-exclude = [
 # Group violations by containing file.
 output-format = "grouped"
 line-length = 120
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 ignore = ["C408"]

tests/test_coxnet.py

@@ -1,6 +1,5 @@
 from dataclasses import dataclass
 from os.path import dirname, join
-from typing import Optional
 
 import numpy as np
 from numpy.testing import assert_array_almost_equal
@@ -68,8 +67,8 @@ def assert_predictions_equal(coxnet, x, expected_pred):
 class CoxnetExpectation:
     alphas: np.ndarray
     coef: pd.DataFrame
-    pred: Optional[np.ndarray] = None
-    dev: Optional[np.ndarray] = None
+    pred: None | np.ndarray = None
+    dev: None | np.ndarray = None
 
 
 class CoxnetCases(FixtureParameterFactory):