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 from pyproject.toml
- Simplify numba dependency to single version without Python constraints
- Update wheel building to use Python 3.10-3.13
- Update GitHub Actions tests to use Python 3.10 and 3.13
- Update docker shared.env to exclude cp39-cp39

Author: benjeffery

.github/workflows/docker/shared.env

@@ -3,5 +3,4 @@ PYTHON_VERSIONS=(
     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, 3.13 ]
+        python: [ "3.10", 3.13 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:

.github/workflows/wheels.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Checkout
         uses: actions/[email protected]
@@ -45,7 +45,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -85,10 +85,10 @@ jobs:
       - name: Checkout
         uses: actions/[email protected]
 
-      - 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
@@ -118,7 +118,7 @@ jobs:
     needs: ['OSX']
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13]
         runner: [macos-13, macos-15]
         include:
           - runner: macos-13
@@ -155,7 +155,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13]
         wordsize: [64]
     steps:
       - name: Download wheels
@@ -179,10 +179,8 @@ jobs:
     needs: ['manylinux']
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13]
         include:
-          - python: 3.9
-            wheel: cp39
           - python: "3.10"
             wheel: cp310
           - python: 3.11

python/CHANGELOG.rst

@@ -10,6 +10,8 @@
   is not the case.
   (:user:`benjeffery`, :issue:`2729`, :issue:`2732`, :pr:`3212`).
 
+- Drop Python 3.9 support, require Python >= 3.10 (:pr:`3267`, :user:`benjeffery`)
+
 
 **Features**
 

python/pyproject.toml

@@ -15,7 +15,6 @@ 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",
@@ -40,7 +39,7 @@ keywords = [
     "phylogenetics",
     "tskit",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "jsonschema>=3.0.0",
     "numpy>=2",
@@ -72,8 +71,7 @@ test = [
     "msgpack==1.1.0",
     "msprime==1.3.4",
     "networkx==3.2.1",
-    "numba==0.61.2; python_version>='3.10'",
-    "numba==0.60.0; python_version=='3.9'",
+    "numba==0.61.2",
     "portion==2.6.0",
     "pytest==8.3.5",
     "pytest-cov==6.0.0",