Add support for Python 3.14

.github/workflows/tests.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: [ "3.10", 3.13 ]
+        python: [ "3.10", 3.14 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:

.github/workflows/wheels.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
     steps:
       - name: Checkout
         uses: actions/checkout@v6.0.2
@@ -51,7 +51,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -125,7 +125,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
         runner: [macos-15, macos-15-intel]
         include:
           - runner: macos-15
@@ -163,7 +163,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
         wordsize: [64]
     steps:
       - name: Download wheels
@@ -188,7 +188,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
+        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
         include:
           - python: "3.10"
             wheel: cp310
@@ -198,6 +198,8 @@ jobs:
             wheel: cp312
           - python: 3.13
             wheel: cp313
+          - python: 3.14
+            wheel: cp314
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v7.0.0

python/CHANGELOG.rst

@@ -8,6 +8,10 @@
   ID is e.g. a population name, rather than silently returning no samples.
   (:user:`hyanwong`, :pr:`3344`)
 
+**Maintenance**
+
+- Add support for Python 3.14
+
 --------------------
 [1.0.0] - 2025-11-27
 --------------------
@@ -22,7 +26,7 @@
 - ``TreeSequence.tables`` now returns a zero-copy immutable view of the tables.
   To get a mutable copy, use ``TreeSequence.dump_tables()``.
   (:user:`benjeffery`, :pr:`3288`, :issue:`760`)
-  
+
 - For a tree sequence to be valid, the mutation parents in the table collection
   must be correct and consistent with the topology of the tree at each mutation site.
   ``TableCollection.tree_sequence()`` will raise a ``_tskit.LibraryError`` if this
@@ -146,7 +150,7 @@
   (:user:`hyanwong`, :pr:`3165`, :issue:`3164`)
 
 - Add ``TreeSequence.map_to_vcf_model`` method to return a mapping of
-  the tree sequence to the VCF model. 
+  the tree sequence to the VCF model.
   (:user:`benjeffery`, :pr:`3163`)
 
 - Use a thin space as the thousands separator in HTML output,
@@ -157,14 +161,14 @@
 
 - Correct assertion message when tables are compared with metadata ignored.
   (:user:`benjeffery`, :pr:`3162`, :issue:`3161`)
-  
-**Breaking changes** 
+
+**Breaking changes**
 
 - ``TreeSequence.write_vcf`` now filters non-sample nodes from individuals
   by default, instead of raising an error. These nodes can be included using the
-  new ``include_non_sample_nodes`` argument. 
+  new ``include_non_sample_nodes`` argument.
   By default individual names (sample IDs) in VCF output are now of the form
-  ``tsk_{individual.id}`` Previously these were always 
+  ``tsk_{individual.id}`` Previously these were always
   ``"tsk_{j}" for j in range(num_individuals)``. This may break some downstream
   code if individuals are specified. To fix, manually specify ``individual_names``
   to the required pattern.

python/pyproject.toml

@@ -19,6 +19,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: 3 :: Only",
     "Development Status :: 5 - Production/Stable",
     "Environment :: Other Environment",
@@ -68,9 +69,9 @@ test = [
     "kastore==0.3.3",
     "lshmm==0.0.8",
     "msgpack==1.1.0",
-    "msprime==1.3.4",
+    "msprime==1.4.0b2",
     "networkx==3.2.1",
-    "numba==0.61.2",
+    "numba==0.63.1",
     "portion==2.6.0",
     "pytest==8.3.5",
     "pytest-cov==6.0.0",
@@ -88,8 +89,8 @@ docs = [
     "sphinx-autodoc-typehints==2.3.0",
     "sphinx-issues==5.0.0",
     "sphinx-argparse==0.5.2",
-    "msprime==1.3.3",
-    "numba==0.61.2",
+    "msprime==1.4.0b2",
+    "numba==0.63.1",
     "sphinx-book-theme",
     "pandas==2.2.3",
 ]
@@ -117,7 +118,7 @@ dev = [
     "xmlunittest",
     "newick",
     "zarr<3",
-    "jupyter-book",
+    "jupyter-book<2",
     "breathe",
     "sphinx-autodoc-typehints",
     "sphinx-issues",

python/tests/test_balance_metrics.py

@@ -192,7 +192,7 @@ def test_b2_base(self, base, expected):
 
     @pytest.mark.parametrize("base", [0, -0.001, -1, -1e-6, -1e200])
     def test_b2_bad_base(self, base):
-        with pytest.raises(ValueError, match="math domain"):
+        with pytest.raises(ValueError):
             self.tree().b2_index(base=base)
 
     def test_b2_base1(self):