tooling: use uv and set up publishing (#9)

* refactor: migrate from rye to uv package manager and update tooling

The commit message reflects a significant change in the project's development
tooling, switching from rye to uv for package management, and replacing
multiple linting tools (pylint, flake8) with ruff for better performance
and maintainability.

* ci: add GitHub Actions workflows for continuous integration and deployment

* chore: remove tox configuration as it's no longer used for test automation

.github/workflows/cd.yml

@@ -0,0 +1,32 @@
+# publish.yml
+
+name: "Publish"
+
+on:
+  release:
+    types: ["published"]
+
+jobs:
+  run:
+    name: "Build and publish release"
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # needed for Trusted Publishing on PyPi
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Build
+        run: uv build
+
+      - name: Publish
+        run: uv publish

.github/workflows/ci.yml

@@ -0,0 +1,60 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install just
+      uses: taiki-e/install-action@just
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
+
+    - name: Set up Python
+      run: uv python install 3.12
+
+    - name: Install dependencies
+      run: uv sync --all-extras --dev
+
+    - name: Lint
+      run: just lint
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install just
+      uses: taiki-e/install-action@just
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: uv sync --all-extras --dev
+
+    - name: Test
+      run: just test

Justfile

@@ -1,29 +1,25 @@
 default:
     @just --list
 
-tox:
-    @tox
-
 test:
-    @pytest -s
+    @uv run pytest
+
+test-s:
+    @uv run pytest -s -o log_cli=True -o log_cli_level=DEBUG
 
-pylint:
-    rye run pylint labfile
+ruff-fix:
+    uv run ruff format labfile
 
-flake8:
-    rye run flake8 labfile
+ruff-check:
+    uv run ruff check labfile
 
 pyright:
-    rye run pyright labfile
+    uv run pyright labfile
 
 lint:
-    just pylint
-    just flake8
+    just ruff-check
     just pyright
 
-
 lint-file file:
-    - pylint {{file}}
-    - flake8 {{file}}
+    - ruff {{file}}
     - pyright {{file}}
-

pyproject.toml

@@ -1,39 +1,54 @@
 [project]
 name = "labfile"
-version = "0.1.0"
-description = "Add your description here"
+description = "A declarative file format for scientific experiments."
 authors = [
     { name = "Rory Byrne", email = "[email protected]" }
 ]
+requires-python = ">=3.8"
 dependencies = [
-    "pydantic>=2.9.2",
     "pydantic-settings>=2.6.1",
     "lark>=1.2.2",
+    "pydantic>=2.10.3",
 ]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: OS Independent",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Scientific/Engineering",
+    "Intended Audience :: Developers",
+    'Intended Audience :: Information Technology',
+    "Typing :: Typed",
+]
+license = "MIT"
 readme = "README.md"
-requires-python = ">= 3.8"
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/flywhl/labfile"
+Repository = "https://github.com/flywhl/labfile"
+Documentation = "https://github.com/flywhl/labfile#readme"
+"Bug Tracker" = "https://github.com/flywhl/labfile/issues"
 
 [build-system]
-requires = ["hatchling"]
+requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
-[tool.rye]
-managed = true
+[tool.hatch.version]
+source = "vcs"
+
+[tool.uv]
 dev-dependencies = [
-    "pytest>=8.3.3",
-    "black>=24.10.0",
-    "pylint>=3.3.1",
-    "isort>=5.13.2",
-    "flake8>=7.1.1",
-    "pyright>=1.1.388",
-    "flake8-pyproject>=1.2.3",
-    "tox>=4.23.2",
-    "coverage>=7.6.4",
-    "pre-commit>=4.0.1",
+    "coverage>=7.6.1",
+    "pre-commit>=3.5.0",
+    "pyright>=1.1.391",
+    "pytest>=8.3.4",
+    "ruff>=0.9.1",
 ]
-
-[tool.hatch.metadata]
-allow-direct-references = true
-
-[tool.hatch.build.targets.wheel]
-packages = ["labfile"]