Support Python 3.13

.cspell/library_terms.txt

@@ -140,6 +140,7 @@ pytest
 PYTHONHASHSEED
 pytorch
 pyupgrade
+pywinpty
 qualnames
 quickstart
 randn

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -45,6 +45,7 @@ body:
         - "3.10"
         - "3.11"
         - "3.12"
+        - "3.13"
     validations:
       required: true
   - type: input

.github/workflows/check_todos.yml

@@ -13,10 +13,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.12
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: 3.12
+        python-version: 3.13
     - name: Upgrade pip
       run: python -m pip install --upgrade pip
     - name: Install Ruff

.github/workflows/coverage.yml

@@ -25,7 +25,7 @@ jobs:
           # `uv` manages its own version of Python.
           # For speed, we use the same version for both, but in principle these could
           # differ.
-          python-version: 3.12
+          python-version: 3.13
       - name: Set up uv cache directory location (Linux/Mac)
         run: echo "UV_CACHE_DIR=${{ runner.temp }}/.uv-cache" >> $GITHUB_ENV
         if: runner.os != 'Windows'

.github/workflows/docs.yml

@@ -14,16 +14,16 @@ jobs:
     runs-on: ubuntu-latest
     env:
       # Set the Python version that `uv` will use for its virtual environment.
-      UV_PYTHON: 3.12
+      UV_PYTHON: 3.13
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
           # Note that this is just the version of Python that we use to run `uv` with.
           # `uv` manages its own version of Python.
           # For speed, we use the same version for both, but in principle these could differ.
-          python-version: 3.12
+          python-version: 3.13
       - name: Set up uv cache directory location
         run: echo "UV_CACHE_DIR=${{ runner.temp }}/.uv-cache" >> $GITHUB_ENV
       - name: Restore uv cache

.github/workflows/pre_commit_autoupdate.yml

@@ -45,10 +45,10 @@ jobs:
           fi
 
       # Pre-commit setup and autoupdate steps
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           # Re-enable when going public
           # cache: pip
       - name: Upgrade Pip

.github/workflows/pre_commit_checks.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       # Set the Python version that `uv` will use for its virtual environment.
-      UV_PYTHON: 3.12
+      UV_PYTHON: 3.13
     steps:
       - uses: actions/checkout@v4
       - name: Set up base Python

.github/workflows/release.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Set up base Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
       - name: Install and upgrade build tools
         run: |
           python -m pip install --upgrade pip
@@ -54,6 +54,7 @@ jobs:
           - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
         os:
           - ubuntu-latest
           - windows-latest

.github/workflows/unittests.yml

@@ -13,12 +13,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # Note that we only do type checking on Python 3.12.
+        # Note that we only do type checking on Python 3.13 (the latest Python version).
         python-version:
           - "3.9"
           - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
         os:
           - ubuntu-latest
           - windows-latest
@@ -65,21 +66,21 @@ jobs:
         --ignore=tests/test_examples.py
         -W "error::vanguard.utils.UnseededRandomWarning"
         -m "no_beartype"
-      if: matrix.python-version == '3.12'
+      if: matrix.python-version == '3.13'
     - name: Test with pytest (and type checking)
       run: >
         uv run pytest
         --ignore=tests/test_examples.py
         -W "error::vanguard.utils.UnseededRandomWarning"
         -m "not no_beartype"
         --beartype-packages="vanguard"
-      if: matrix.python-version == '3.12'
+      if: matrix.python-version == '3.13'
     - name: Run all tests
       run: >
         uv run pytest
         --ignore=tests/test_examples.py
         -W "error::vanguard.utils.UnseededRandomWarning"
-      if: matrix.python-version != '3.12'
+      if: matrix.python-version != '3.13'
     - name: Minimize UV cache
       run: uv cache prune --ci
       if: always()

.github/workflows/unittests_lowest.yml

@@ -22,6 +22,7 @@ jobs:
           - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
         os:
           - ubuntu-latest
           - windows-latest

.github/workflows/uv_lock_autoupdate.yml

@@ -47,10 +47,10 @@ jobs:
           fi
 
       # uv setup and lockfile upgrading steps
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
       - name: Upgrade Pip
         run: python -m pip install --upgrade pip

.python-version

@@ -1 +1 @@
-3.12
+3.13

.readthedocs.yaml

@@ -6,7 +6,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.13"
 
 sphinx:
   configuration: docs/source/conf.py

CHANGELOG.md

@@ -10,7 +10,7 @@ Version 4 will be the first stable version.
 
 ### Added
 
--
+- Support for Python 3.13. (https://github.com/gchq/Vanguard/pull/511)
 
 ### Fixed
 
@@ -22,7 +22,8 @@ Version 4 will be the first stable version.
 
 ### Removed
 
--
+- [BREAKING CHANGE] Removed support for old versions of some dependencies; most importantly, we no longer support
+  NumPy 1.x. (https://github.com/gchq/Vanguard/pull/511)
 
 ### Deprecated
 

CONTRIBUTING.md

@@ -403,7 +403,7 @@ pip install -r requirements-docs.txt --no-deps
 from the repo root. Note that the pinned dependencies are not guaranteed to work on Windows or macOS.
 
 In both cases, these commands should be run in a fresh virtual environment (to avoid any issues with already-existing
-packages), and on Python 3.12.
+packages), and on Python 3.13.
 
 ### Building the documentation
 

pyproject.toml

@@ -20,6 +20,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Typing :: Typed",
 ]
 license = {file = "LICENSE.md"}
@@ -35,17 +36,18 @@ dependencies = [
     "kmedoids>=0.3.3",  # first version with prebuilt wheels; earlier versions require a rust toolchain to build
     "kmedoids>=0.4; python_version>='3.11'",  # earlier versions don't have prebuilt wheels for python 3.11
     "kmedoids>=0.4.4; python_version>='3.12'",  # earlier versions don't have prebuilt wheels for python 3.12
-    "matplotlib>=3.5",  # earlier versions don't install properly on Windows
-    "matplotlib>=3.6; python_version>='3.11'",  # earlier versions don't install properly on Windows
-    "numpy>=1.21",  # numpy.typing introduced in 1.21
-    "numpy>=1.26; python_version>='3.12'",  # 1.25 and earlier require distutils, which was removed in 3.12
+    "kmedoids>=0.5.3; python_version>='3.13'",  # earlier versions don't have prebuilt wheels for python 3.13
+    "matplotlib>=3.8.4",  # first version to support numpy 2
+    "numpy>=2",  # modern versions of packages are incompatible with numpy<2
+    "numpy>=2.1.0; python_version>='3.13'",  # first version to support python 3.13
     "pandas>=2",
+    "pandas>=2.2.3; python_version>='3.13'",  # earlier versions don't provide prebuilt wheels for python 3.13
     "scikit-learn>=1.5.0",  # CVE-2024-5206 affects versions earlier than 1.5.0
-    "scipy>=1.4",  # earlier versions fail to build with recent setuptools versions
-    "scipy>=1.12; python_version>='3.12'",  # earlier versions don't provide prebuilt wheels for python 3.12
-    "torch>=2.2",  # torch.optim.LRScheduler made public in 2.0.0;
-                   #   versions <2.2 have issues with C library dependencies in our CI
-    "typing_extensions>=4.4",  # @override introduced in 4.4
+    "scikit-learn>=1.6.0; python_version>='3.13'",  # earlier versions don't provide prebuilt wheels for python 3.13
+    "scipy>=1.13",  # first version to support numpy 2
+    "scipy>=1.14.1; python_version>='3.13'",  # earlier versions don't provide prebuilt wheels for python 3.13
+    "torch>=2.6",  # earlier versions have issues in CI in lower-bound tests
+    "typing_extensions>=4.12",  # ParamSpec behaviour improved in 4.12
     "urllib3>=2.0.4",  # BaseHttpResponse added to urllib3.__all__ in 2.0.4
 ]
 
@@ -117,7 +119,6 @@ constraint-dependencies = [
     "six>=1.16; python_version>='3.10'",  # earlier versions don't work on 3.10+
     "pyzmq>=26",
     "contourpy>=1.1; python_version>='3.11'",
-    "nvidia-nvjitlink-cu12>=12.6.77",  # torch CUDA dependency
     "lxml>=4.7.1",  # earlier versions fail to build to missing libxml2
     "argon2-cffi>=19", # earlier versions have issues building on Linux
     "bleach>=1",  # some pre-1.0 versions fail to build
@@ -127,8 +128,12 @@ constraint-dependencies = [
     "pywin32>=302; python_version>='3.10'",  # first version to support 3.10
     "pywin32>=303; python_version>='3.11'",  # first version to support 3.11
     "pywin32>=306; python_version>='3.12'",  # first version to support 3.12
+    "pywin32>=307; python_version>='3.13'",  # first version to support 3.13
     "wheel>=0.30",  # picking a too-low version of this was causing CI failures that couldn't be replicated locally,
                     # so this is a guessed lower bound
+    "cffi>=1.17; python_version>='3.13'",
+    "pywinpty>=2.0.14; python_version>='3.13'",
+    "pillow>=11; python_version>='3.13'",
 ]
 
 # force the lockfile to be split by Python version, ensuring we get the latest dependencies for each version

requirements-docs.txt

@@ -3,7 +3,7 @@
 .
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
-appnope==0.1.4 ; sys_platform == 'darwin'
+appnope==0.1.4 ; (python_full_version < '3.13' and sys_platform == 'darwin') or (os_name != 'nt' and sys_platform == 'darwin')
 asttokens==3.0.0
 attrs==25.1.0
 babel==2.17.0
@@ -69,18 +69,19 @@ networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version >= '3.10'
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.3 ; python_full_version >= '3.10'
-nvidia-cublas-cu12==12.1.3.1 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cuda-cupti-cu12==12.1.105 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cuda-nvrtc-cu12==12.1.105 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cuda-runtime-cu12==12.1.105 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cudnn-cu12==9.1.0.70 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cufft-cu12==11.0.2.54 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-curand-cu12==10.3.2.106 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cusolver-cu12==11.4.5.107 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-cusparse-cu12==12.1.0.106 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-nccl-cu12==2.20.5 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-nvjitlink-cu12==12.8.61 ; platform_machine == 'x86_64' and sys_platform == 'linux'
-nvidia-nvtx-cu12==12.1.105 ; platform_machine == 'x86_64' and sys_platform == 'linux'
+nvidia-cublas-cu12==12.4.5.8 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cuda-cupti-cu12==12.4.127 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cuda-nvrtc-cu12==12.4.127 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cuda-runtime-cu12==12.4.127 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cudnn-cu12==9.1.0.70 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cufft-cu12==11.2.1.3 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-curand-cu12==10.3.5.147 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cusolver-cu12==11.6.1.9 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cusparse-cu12==12.3.1.170 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-cusparselt-cu12==0.6.2 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-nccl-cu12==2.21.5 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-nvjitlink-cu12==12.4.127 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+nvidia-nvtx-cu12==12.4.127 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
 packaging==24.2
 pandas==2.2.3
 pandocfilters==1.5.1
@@ -107,7 +108,7 @@ requests==2.32.3
 rpds-py==0.22.3
 scikit-learn==1.6.1
 scipy==1.13.1 ; python_full_version < '3.10'
-scipy==1.15.1 ; python_full_version >= '3.10'
+scipy==1.15.2 ; python_full_version >= '3.10'
 setuptools==75.8.0 ; python_full_version >= '3.12'
 six==1.17.0
 snowballstemmer==2.2.0
@@ -125,16 +126,16 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
-sympy==1.13.3
+sympy==1.13.1
 threadpoolctl==3.5.0
 tinycss2==1.4.0
 tomli==2.2.1 ; python_full_version < '3.11'
-torch==2.4.1
+torch==2.6.0
 tornado==6.4.2
 tqdm==4.67.1
 traitlets==5.14.3
-triton==3.0.0 ; python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux'
-typeguard==4.4.1 ; python_full_version < '3.10'
+triton==3.2.0 ; (python_full_version < '3.13' and platform_machine == 'x86_64' and sys_platform == 'linux') or (os_name != 'nt' and platform_machine == 'x86_64' and sys_platform == 'linux')
+typeguard==4.4.2 ; python_full_version < '3.10'
 typing-extensions==4.12.2
 tzdata==2025.1
 urllib3==2.3.0