Update for Python 3.14

.github/workflows/coverage.yaml

@@ -23,7 +23,7 @@ jobs:
         id: setuppy
         uses: actions/setup-python@v4
         with:
-          python-version: "3.12"
+          python-version: "3.14"
 
       - name: "Set up Poetry"
         uses: abatilo/actions-poetry@v2

.github/workflows/lint-and-type.yaml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.14"]
     runs-on: ubuntu-latest
 
     steps:
@@ -48,7 +48,7 @@ jobs:
         run: poetry run black --check turtlemd
 
       - name: "Run ruff"
-        run: poetry run ruff turtlemd
+        run: poetry run ruff check turtlemd
 
       - name: "Run mypy"
         run: poetry run mypy turtlemd

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.12", "3.13", "3.14"]
     runs-on: ubuntu-latest
 
     steps:

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
     hooks:
       - id: black-jupyter
         # It is recommended to specify the latest version of Python
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.11
+        language_version: python3.14

Makefile

@@ -13,7 +13,7 @@ coverage-print:
 	pytest --cov-report html --cov=turtlemd -rP tests/
 
 ruff:
-	poetry run ruff turtlemd
+	poetry run ruff check turtlemd
 
 black:
 	poetry run black --check turtlemd

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "turtlemd"
-version = "2023.3.1"
+version = "2025.1"
 description = "A slow molecular dynamics library for testing"
 authors = [
     "Daniel Zhang <daniel.t.zhang@ntnu.no>",
@@ -11,13 +11,13 @@ license = "MIT"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.13"
+python = ">=3.12,<3.15"
 numpy = "^1.24.2"
 
 [tool.poetry.group.dev.dependencies]
-ruff = "^0.0.261"
-black = "^23.3.0"
-mypy = "^1.2.0"
+ruff = "^0.14.0"
+black = "^25.9.0"
+mypy = "^1.18.0"
 pytest = "^7.3.1"
 pytest-cov = "^4.0.0"
 pytest-randomly = "^3.12.0"
@@ -27,12 +27,13 @@ flake8 = "^6.0.0"
 
 [tool.ruff]
 line-length = 79
+
+[tool.ruff.lint]
 select = ["F", "E", "W", "I001", "UP"]
-ignore-init-module-imports = true
 
 [tool.black]
 line-length = 79
-target-version = ["py310", "py311", "py312"]
+target-version = ["py312", "py313", "py314"]
 
 [tool.mypy]
 warn_unused_ignores = true

turtlemd/__init__.py

@@ -1,4 +1,5 @@
 """TurtleMD is a slow MD library for testing."""
+
 from .version import __version__
 
 __all__ = ["__version__"]

turtlemd/integrators.py

@@ -1,4 +1,5 @@
 """Definition of time integrators."""
+
 import logging
 from abc import ABC, abstractmethod
 from dataclasses import dataclass, field

turtlemd/potentials/lennardjones.py

@@ -1,4 +1,5 @@
 """Module defining a Lennard-Jones pair potential."""
+
 import itertools
 import logging
 from typing import Any

turtlemd/potentials/potential.py

@@ -3,6 +3,7 @@
 This module defines the generic class for potential functions.
 This class is sub-classed in all potential functions.
 """
+
 from __future__ import annotations
 
 import logging

turtlemd/potentials/well.py

@@ -12,6 +12,7 @@
 * DoubleWellPair (:py:class:`.DoubleWellPair`)
     This class defines a double well pair potential.
 """
+
 import logging
 
 import numpy as np
@@ -276,9 +277,7 @@ def force(self, system: System) -> tuple[np.ndarray, np.ndarray]:
                 delta = box.pbc_dist(particles.pos[i] - particles.pos[j])
                 delr = np.sqrt(np.dot(delta, delta))
                 diff = delr - rwidth
-                forceij = (
-                    height4 * (1.0 - diff**2 / width2) * (diff / width2)
-                )
+                forceij = height4 * (1.0 - diff**2 / width2) * (diff / width2)
                 forceij = forceij * delta / delr
                 forces[i] += forceij
                 forces[j] -= forceij

turtlemd/simulation/mdsimulation.py

@@ -1,4 +1,5 @@
 """Definition of a simulation."""
+
 from __future__ import annotations
 
 import logging

turtlemd/simulation/stopping.py

@@ -1,4 +1,5 @@
 """Definitions for stopping a simulation."""
+
 from __future__ import annotations
 
 import logging

turtlemd/system/__init__.py

@@ -1,4 +1,5 @@
 """For importing the most commonly used system methods."""
+
 from .box import Box
 from .particles import Particles
 from .system import System

turtlemd/system/box.py

@@ -1,4 +1,5 @@
 """Define a simulation box."""
+
 import itertools
 import logging
 from abc import ABC, abstractmethod

turtlemd/system/particles.py

@@ -3,6 +3,7 @@
 Tha particle list collects the mass, positions, velocities,
 forces, types, etc. for a collection of particles.
 """
+
 from collections.abc import Iterator
 from typing import SupportsIndex
 

turtlemd/system/system.py

@@ -1,4 +1,5 @@
 """Definition of the simulation system."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any, TypedDict

turtlemd/tools/tools.py

@@ -1,4 +1,5 @@
 """Some helper methods for setting up simulations."""
+
 import itertools
 
 import numpy as np

turtlemd/tools/xyz.py

@@ -1,4 +1,5 @@
 """Methods to read particles from xyz-files."""
+
 import logging
 import pathlib
 from collections.abc import Iterator

turtlemd/version.py

@@ -1,4 +1,5 @@
 """Version information."""
+
 from importlib import metadata
 
 __version__ = metadata.version("turtlemd")