ci: update CI configuration for testing across Python 3.10 to 3.14

.github/workflows/ci.yml

@@ -22,22 +22,34 @@ jobs:
         run: pipx run pre-commit run --all-files
 
   test:
+    name: ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.resolution }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.11", "3.13"]
+        # ubuntu: full python range x both resolutions
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        resolution: [lowest-direct, highest]
+        # windows/macos: only the endpoints, highest resolution
+        include:
+          - { os: windows-latest, python-version: "3.10", resolution: highest }
+          - { os: windows-latest, python-version: "3.14", resolution: highest }
+          - { os: macos-latest, python-version: "3.10", resolution: highest }
+          - { os: macos-latest, python-version: "3.14", resolution: highest }
+
+    env:
+      UV_RESOLUTION: ${{ matrix.resolution }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
       - name: Test with coverage
-        run: uv run pytest -v --cov=spatial_graph --cov-report=xml
+        run: uv run --no-dev --group test pytest -v --cov=spatial_graph --cov-report=xml
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -7,21 +7,21 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.7
+    rev: v0.15.16
     hooks:
       - id: ruff-check
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v2.1.0
     hooks:
       - id: mypy

pyproject.toml

@@ -10,7 +10,7 @@ name = "spatial-graph"
 dynamic = ["version"]
 description = "A spatial graph datastructure for python."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "MIT" }
 authors = [
   { email = "funkej@janelia.hhmi.org", name = "Jan Funke" },
@@ -20,14 +20,24 @@ classifiers = [
   "Development Status :: 3 - Alpha",
   "Intended Audience :: Developers",
   "License :: OSI Approved :: MIT License",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Typing :: Typed",
 ]
-dependencies = ["witty>=v0.3.0", "CT3>=3.3.3", "numpy", "setuptools>=75.8.0"]
+dependencies = [
+  "witty>=v0.3.0",
+  "CT3>=3.3.3",
+  "numpy>=2.3.2; python_version >= '3.14'",
+  "numpy>=2.1.0; python_version >= '3.13'",
+  "numpy>=1.26.0; python_version >= '3.12'",
+  "numpy>=1.23.2; python_version >= '3.11'",
+  "numpy>=1.21.2",
+  "setuptools>=75.8.0",
+  "typing_extensions>=4.5.0",  # witty<=0.3.1 imports it without declaring it
+]
 
 [dependency-groups]
 test = ["pytest>=8.3.5", "pytest-cov>=6.1.1"]
@@ -36,7 +46,7 @@ dev = [
   { include-group = "test" },
   "ipython>=8.18.1",
   "mypy>=1.15.0",
-  "pre-commit>=4.2.0",
+  "prek>=0.4.4",
   "pytest-benchmark>=5.1.0",  # specifically excluded from test group for ci
   "ruff>=0.11.10",
 ]
@@ -54,7 +64,7 @@ homepage = "https://github.com/funkelab/spatial_graph"
 repository = "https://github.com/funkelab/spatial_graph"
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 line-length = 88
 fix = true
 unsafe-fixes = true