Drop Python 3.9 support, update to Python 3.10-3.13

- Update pyproject.toml requires-python to >=3.10
- Remove Python 3.9 classifier, add Python 3.13 classifier
- Update wheel building to use Python 3.10-3.13
- Update GitHub Actions tests to use Python 3.10 and 3.13
- Update CircleCI to use Python 3.10
- Update docker shared.env to include cp313 and exclude cp39

Author: benjeffery

.circleci/config.yml

@@ -6,7 +6,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.9
+      - image: cimg/python:3.10
     steps:
       - checkout
 
@@ -25,7 +25,7 @@ jobs:
       - run:
           name: Install test dependencies
           command: |
-              pyenv global 3.9
+              pyenv global 3.10
               pip install uv
               uv pip install --system -r pyproject.toml --extra test
               pyenv rehash

.github/workflows/docker/shared.env

@@ -1,6 +1,6 @@
 PYTHON_VERSIONS=(
+    cp313-cp313
     cp312-cp312
     cp311-cp311
     cp310-cp310
-    cp39-cp39
 )

.github/workflows/tests.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: [ 3.9, "3.12" ]
+        python: [ "3.10", 3.13 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:
@@ -46,7 +46,6 @@ jobs:
       - name: Install cyvcf2 #Fails if done via conda due to no windows support.
         if: matrix.os != 'windows-latest'
         run: |
-          #Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
           uv pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3 
 
       - name: Install sgkit only on windows

.github/workflows/wheels.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: ["3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Checkout
         uses: actions/[email protected]
@@ -44,7 +44,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: ["3.10", 3.11, 3.12, 3.13]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -79,10 +79,10 @@ jobs:
         with:
             submodules: true
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/[email protected]
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Build sdist
         shell: bash
@@ -112,7 +112,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: ["3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Download wheels
         uses: actions/[email protected]
@@ -135,7 +135,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: ["3.10", 3.11, 3.12, 3.13]
         wordsize: [64]
     steps:
       - name: Download wheels
@@ -161,7 +161,7 @@ jobs:
     needs: ['manylinux']
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: ["3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Download wheels
         uses: actions/[email protected]

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.4.2] - 2025-XX-XX
+
+** Changes **
+
+- Drop Python 3.9 support, require Python >= 3.10 ({pr}`1044`, {user}`benjeffery`)
+
 ## [0.4.1] - 2024-04-19
 
 ** Changes **

pyproject.toml

@@ -18,16 +18,16 @@ authors = [
 ]
 description = "Infer tree sequences from genetic variation data."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {text = "GNU GPLv3+"}
 classifiers = [
     "Programming Language :: C",
     "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",
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
     "Development Status :: 3 - Alpha",