Add support for Py3.13

.github/workflows/docker/shared.env

@@ -3,5 +3,6 @@ PYTHON_VERSIONS=(
     cp310-cp310
     cp311-cp311
     cp312-cp312
+    cp313-cp313
 )
 GSL_VERSION=2.6

.github/workflows/docs.yml

@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/setup-python@v5.4.0
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: "pip"
 
       - name: Create venv and install deps (one by one to avoid conflict errors)

.github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.9, 3.12 ]
+        python: [ 3.9, 3.13 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:

.github/workflows/wheels.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-13, macos-14, macos-15]
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: [3.9, "3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Checkout
         uses: actions/checkout@v4.2.2
@@ -104,7 +104,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-13, macos-14, macos-15]
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: [3.9, "3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v4.2.0
@@ -130,7 +130,7 @@ jobs:
     needs: ['manylinux']
     strategy:
       matrix:
-        python: [3.9, "3.10", 3.11, 3.12]
+        python: [3.9, "3.10", 3.11, 3.12, 3.13]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v4.2.0

.mergify.yml

@@ -8,22 +8,22 @@ queue_rules:
       - status-success=Docs
       - status-success=Lint
       - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.13, macos-latest)
       - status-success=Python (3.9, ubuntu-24.04)
-      - status-success=Python (3.12, ubuntu-24.04)
+      - status-success=Python (3.13, ubuntu-24.04)
       - status-success=Python (3.9, windows-latest)
-      - status-success=Python (3.12, windows-latest)
+      - status-success=Python (3.13, windows-latest)
       - "status-success=ci/circleci: build"
     merge_conditions:
       - "#approved-reviews-by>=1"
       - status-success=Docs
       - status-success=Lint
       - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.13, macos-latest)
       - status-success=Python (3.9, ubuntu-24.04)
-      - status-success=Python (3.12, ubuntu-24.04)
+      - status-success=Python (3.13, ubuntu-24.04)
       - status-success=Python (3.9, windows-latest)
-      - status-success=Python (3.12, windows-latest)
+      - status-success=Python (3.13, windows-latest)
       - "status-success=ci/circleci: build"
     merge_method: rebase
     update_method: rebase

CHANGELOG.md

@@ -8,6 +8,8 @@
 - The `FixedPedigree` simulation model now supports internal samples ({issue}`1855`,
   {pr}`2321`, {pr}`2326`, {pr}`2388`, {user}`abureau`, {user}`jeromekelleher`).
 
+- Add support and wheels for Python3.13
+
 **Breaking changes**:
 
 - The `.asdict()` methods for Demography, Population, and Event classes in the

pyproject.toml

@@ -15,6 +15,7 @@ classifiers = [
     "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",
     "Development Status :: 5 - Production/Stable",
     "Environment :: Other Environment",

requirements/CI-complete/requirements.txt

@@ -1,12 +1,12 @@
 bintrees==2.2.0
 daiquiri==3.3.0
 demes==0.2.3
-mypy==1.15.0
+mypy==1.17.0
 newick==1.10.0
-pytest==8.3.5
-pytest-cov==6.0.0
-pytest-xdist==3.6.1
+pytest==8.4.1
+pytest-cov==6.2.1
+pytest-xdist==3.8.0
 python_jsonschema_objects==0.5.7
-scipy==1.14.0
-tskit==0.6.0
+scipy==1.15.3
+tskit==0.6.4
 kastore==0.3.3

requirements/CI-docs/requirements.txt

@@ -2,11 +2,12 @@ daiquiri==3.3.0
 demes==0.2.3
 demesdraw==0.4.0
 jupyter-book==1.0.4.post1
-networkx==3.4.2
-matplotlib==3.10.1
+networkx==3.5
+matplotlib==3.10.3
 newick==1.10.0
+setuptools==80.9.0
 sphinx-argparse==0.5.2
 sphinx-book-theme # not pinned to enable easy updates
-sphinx-issues==5.0.0
-tskit==0.6.0
-scipy==1.15.2
+sphinx-issues==5.0.1
+tskit==0.6.4
+scipy==1.16.1

requirements/CI-tests-pip/requirements.txt

@@ -1,9 +1,12 @@
 bintrees==2.2.0
-daiquiri==3.2.5.1
+daiquiri==3.2.5.1; python_version<="3.9"
+daiquiri==3.3.0; python_version>"3.9"
 kastore==0.3.3
 newick==1.10.0
-pytest==8.3.5
-pytest-xdist==3.6.1
+pytest==8.4.1
+pytest-xdist==3.8.0
 python_jsonschema_objects==0.5.7
-scipy==1.13.1
-tskit==0.6.0
+setuptools==80.9.0
+scipy==1.13.1; python_version<="3.9"
+scipy==1.16.1; python_version>"3.9"
+tskit==0.6.4