Drop Python 3.9 and 3.10; bump to v3.6.0

Raises requires-python from >=3.9 to >=3.11.

Why:
  Python 3.9 has been EOL since October 2025.
  Python 3.10 EOLs October 2026 (~5 months out).
  Several upstream packages (pillow 12.2+, matplotlib 3.10+)
  no longer support 3.9 or 3.10, leaving the Dependabot
  resolver unable to find a coherent dependency graph and
  preventing security-fix updates from landing on uv.lock.

  Dropping these two versions both unblocks the resolver and
  reduces the duplicated-package noise in uv.lock (pillow has
  one entry instead of two python_full_version splits, etc.).

  Python 3.11 floor gives ~17 months of runway until EOL
  (October 2027); long enough to not have to revisit this
  routinely.

Files updated:
  pyproject.toml
    - requires-python = ">=3.11"
    - classifiers: drop 3.9/3.10, add 3.14
    - cibuildwheel.build: cp311 / cp312 / cp313 / cp314
    - tool.black.target-version: py311
    - tool.mypy.python_version: 3.11
    - version: 3.5.2 -> 3.6.0
  CMakeLists.txt: KALIGN_LIBRARY_VERSION 3.5.2 -> 3.6.0
  build.zig: kalignPackageVersion 3.5.2 -> 3.6.0
  .github/workflows/python.yml: matrix 3.11..3.14
  .github/workflows/wheels.yml: CIBW_BUILD + matrix 3.11..3.14
  uv.lock: regenerated against the new floor (single-graph
           entries replace the python<3.10 split duplicates).
  ChangeLog: new 3.6.0 release entry.

This is a breaking change for users on Python 3.9 or 3.10 —
hence the minor version bump (3.6.0) rather than a patch.

Verified: kalign --version reports 3.6.0; kalign.__version__
reports 3.6.0. Full check-local.sh run pending.

Author: TimoLassmann

.github/workflows/python.yml

@@ -54,7 +54,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
     - uses: actions/checkout@v5

.github/workflows/wheels.yml

@@ -56,7 +56,7 @@ jobs:
 
     - name: Build wheels
       env:
-        CIBW_BUILD: cp39-* cp310-* cp311-* cp312-* cp313-*
+        CIBW_BUILD: cp311-* cp312-* cp313-* cp314-*
         CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"
         CIBW_ARCHS: ${{ matrix.cibw_archs }}
         # Disable OpenMP on macOS to avoid libomp.dylib conflicts
@@ -133,7 +133,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-14]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

CMakeLists.txt

@@ -12,8 +12,8 @@ include(CMakePackageConfigHelpers)
 include(GenerateExportHeader)
 
 set(KALIGN_LIBRARY_VERSION_MAJOR 3)
-set(KALIGN_LIBRARY_VERSION_MINOR 5)
-set(KALIGN_LIBRARY_VERSION_PATCH 2)
+set(KALIGN_LIBRARY_VERSION_MINOR 6)
+set(KALIGN_LIBRARY_VERSION_PATCH 0)
 set(KALIGN_LIBRARY_VERSION_STRING ${KALIGN_LIBRARY_VERSION_MAJOR}.${KALIGN_LIBRARY_VERSION_MINOR}.${KALIGN_LIBRARY_VERSION_PATCH})
 
 

ChangeLog

@@ -1,5 +1,17 @@
 2026-05-16  Timo Lassmann  <timolassmann@icloud.com>
 
+	* version 3.6.0 - Drop Python 3.9/3.10 support; CI Node 24 upgrade
+	- Minimum Python version raised to 3.11. Python 3.9 reached EOL in
+	  October 2025 and 3.10 reaches EOL in October 2026; both are now
+	  beyond their supported lifecycle for upstream wheels (pillow,
+	  matplotlib). Wheels and CI matrices now target 3.11 / 3.12 / 3.13
+	  / 3.14.
+	- GitHub Actions updated to Node.js 24 successor versions
+	  (checkout v5, setup-python v6, upload/download-artifact v5,
+	  codecov v5) ahead of the 2026-06-02 forced Node 24 switch.
+	- Drive-by: dropped redundant `brew install cmake` on macOS-latest
+	  runners (cmake is preinstalled).
+
 	* version 3.5.2 - Four-mode preset system, threadpool, hardening
 	Algorithm and presets
 	- Four mode presets stable for protein and nucleotide:

build.zig

@@ -1,6 +1,6 @@
 const std = @import("std");
 
-const kalignPackageVersion = "3.5.2";
+const kalignPackageVersion = "3.6.0";
 
 const targets: []const std.Target.Query = &.{
     .{ .cpu_arch = .aarch64, .os_tag = .macos },

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "kalign-python"
-version = "3.5.2"
+version = "3.6.0"
 description = "Python wrapper for the Kalign multiple sequence alignment engine"
 readme = "README-python.md"
 license = "Apache-2.0"
@@ -45,16 +45,15 @@ classifiers = [
     "Programming Language :: C",
     "Programming Language :: C++",
     "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",
+    "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: Implementation :: CPython",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Software Development :: Libraries :: Python Modules"
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 dependencies = [
     "numpy>=1.19.0",
 ]
@@ -107,8 +106,7 @@ Repository = "https://github.com/TimoLassmann/kalign"
 Changelog = "https://github.com/TimoLassmann/kalign/blob/main/ChangeLog"
 
 [tool.scikit-build]
-# Wheel settings - removed py-api to build version-specific wheels
-# wheel.py-api = "cp39"
+# Wheel settings - build version-specific wheels (no py-api).
 
 # CMake settings
 cmake.build-type = "Release"
@@ -145,8 +143,8 @@ logging.level = "DEBUG"
 BUILD_PYTHON_MODULE = "ON"
 
 [tool.cibuildwheel]
-# Build wheels for Python 3.9+
-build = "cp39-* cp310-* cp311-* cp312-* cp313-*"
+# Build wheels for Python 3.11+
+build = "cp311-* cp312-* cp313-* cp314-*"
 
 # Skip 32-bit builds (PyPy wheels are not built by default)
 skip = "*-win32 *-manylinux_i686"
@@ -191,7 +189,7 @@ addopts = [
 
 [tool.black]
 line-length = 88
-target-version = ["py39"]
+target-version = ["py311"]
 include = '\.pyi?$'
 extend-exclude = '''
 /(
@@ -208,7 +206,7 @@ extend-exclude = '''
 '''
 
 [tool.mypy]
-python_version = "3.9"
+python_version = "3.11"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true