Merge pull request #21 from tlambert03/src-layout

build: move to src layout, make compatible with uv sync (and use on CI)

Author: tlambert03

.cruft.json

@@ -29,20 +29,17 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.11", "3.13"]
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          pip install ".[dev]"
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
       - name: Test with pytest
-        run: |
-          pytest --color=yes -v tests
+        run: uv run pytest
 
   deploy:
     name: Deploy
@@ -58,21 +55,19 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
-      - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.x"
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
 
       - name: 👷 Build
-        run: |
-          python -m pip install build
-          python -m build
+        run: uv build
 
       - name: 🚢 Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-           password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}
 
       - uses: softprops/action-gh-release@v2
         with:

.github/workflows/ci.yaml

@@ -11,3 +11,6 @@ build
 dist
 .vscode
 docs/_build/
+
+# remove me to enforce synchrony across development environments
+uv.lock

.gitignore

@@ -15,7 +15,7 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.5
+    rev: v0.11.10
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

.pre-commit-config.yaml

@@ -13,15 +13,34 @@ authors = [
   { email = "funkej@janelia.hhmi.org", name = "Jan Funke" },
   { email = "talley.lambert@gmail.com", name = "Talley Lambert" },
 ]
-dependencies = ["witty>=v0.2.0", "CT3", "numpy", "setuptools>=75.8.0"]
+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",
+  "Typing :: Typed",
+]
+dependencies = ["witty>=v0.2.1", "CT3>=3.3.3", "numpy", "setuptools>=75.8.0"]
+
+[dependency-groups]
+dev = [
+  "ipython>=8.18.1",
+  "mypy>=1.15.0",
+  "pre-commit>=4.2.0",
+  "pytest>=8.3.5",
+  "pytest-cov>=6.1.1",
+  "ruff>=0.11.10",
+]
+
 
 [project.urls]
 homepage = "https://github.com/funkelab/spatial_graph"
 repository = "https://github.com/funkelab/spatial_graph"
 
-[project.optional-dependencies]
-dev = ["pytest>=8.3.4", "ruff", "mypy", "pre-commit"]
-
 [tool.ruff]
 target-version = "py39"
 line-length = 88
@@ -47,4 +66,8 @@ strict = false
 disallow_any_generics = false
 disallow_subclassing_any = false
 show_error_codes = true
-pretty = true
+pretty = true
+
+[tool.pytest.ini_options]
+addopts = "-v --color=yes"
+filterwarnings = ["error", "ignore:'cgi' is deprecated"]