Use uv (#504)

Fixes #501. To do: - [ ] Adapt workflow to setup access to PyPI (see https://docs.astral.sh/uv/guides/publish/#publishing-a-package) - [ ] Optimize tests (currently, I'm using `uv pip ...`, but I think this should be replaced with `uv run ...` - [ ] Bump any package versions and/or Python? - [ ] Use Ruff instead of Black?

Author: tompollard

.github/workflows/run-tests.yml

@@ -19,25 +19,19 @@ jobs:
  os: [windows-latest, ubuntu-latest, macos-latest]
  python-version: ["3.8", "3.9", "3.10", "3.11"]
  steps:
- - uses: actions/checkout@v3
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip poetry
- pip install ".[dev]"
+ - uses: actions/checkout@v4
+ - name: Setup uv
+ uses: astral-sh/setup-uv@v3
+ - name: Install Python ${{ matrix.python-version }}
+ run: uv python install ${{ matrix.python-version }}
  - name: Install libsndfile
  if: startsWith(matrix.os, 'ubuntu')
  run: |
  sudo apt-get install -y libsndfile1
  - name: Run tests
- run: pytest
- - name: Validate poetry file
- run: poetry check
+ run: uv run --extra dev pytest
  - name: Check source code format
- run: black --check --diff .
+ run: uv run --extra dev black --check --diff .
 
  test-deb10-i386:
  runs-on: ubuntu-latest

.gitignore

@@ -72,6 +72,3 @@ target/
 
 # pyenv
 .python-version
-
-# Poetry
-poetry.lock

DEVELOPING.md

@@ -16,20 +16,17 @@ black .
 
 ## Package and Dependency Management
 
-This project uses [poetry](https://python-poetry.org/docs/) for package management and distribution.
+This project uses [uv](https://docs.astral.sh/uv/) for package management and distribution.
 
-Development dependencies are specified as optional dependencies, and then added to the "dev" extra group in the [pyproject.toml](./pyproject.toml) file.
+Development dependencies are specified as optional dependencies, at least for now and until [development dependencies](https://docs.astral.sh/uv/concepts/dependencies/#development-dependencies) become more widely used.
 
 ```sh
-# Do NOT use: poetry add <somepackage> --dev
-poetry add --optional <somepackage>
+uv add <somepackage> --optional <somegroup>
 ```
 
-The `[tool.poetry.dev-dependencies]` attribute is NOT used because of a [limitation](https://github.com/python-poetry/poetry/issues/3514) that prevents these dependencies from being pip installable. Therefore, dev dependencies are not installed when purely running `poetry install`, and the `--no-dev` flag has no meaning in this project.
-
 ## Creating Distributions
 
-Make sure the versions in [version.py](./wfdb/version.py) and [pyproject.toml](./pyproject.toml) are updated and kept in sync.
+Make sure to update the version in [version.py](./wfdb/version.py) accordingly.
 
 It may be useful to publish to testpypi and preview the changes before publishing to PyPi. However, the project dependencies likely will not be available when trying to install from there.
 
@@ -47,10 +44,10 @@ poetry config pypi-token.test-pypi <my-testpypi-token>
 To build and upload a new distribution:
 
 ```sh
-poetry build
+uv build
 
-poetry publish -r test-pypi
-poetry publish
+uv publish --publish-url https://test.pypi.org/legacy/
+uv publish
 ```
 
 ## Creating Documentation

pyproject.toml

@@ -1,37 +1,49 @@
-[tool.poetry]
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
 name = "wfdb"
-version = "4.1.2"
 description = "The WFDB Python package: tools for reading, writing, and processing physiologic signals and annotations."
-authors = ["The Laboratory for Computational Physiology <contact@physionet.org>"]
+authors = [{name = "The Laboratory for Computational Physiology", email = "contact@physionet.org"}]
+license = {text = "MIT License"}
 readme = "README.md"
+requires-python = ">= 3.8"
+dependencies = [
+ "numpy >= 1.10.1, < 2.0.0",
+ "scipy >= 1.0.0",
+ "pandas >= 1.3.0",
+ "soundfile >= 0.10.0",
+ "matplotlib >= 3.2.2",
+ "requests >= 2.8.1",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+dev = [
+ "pytest >= 7.1.1",
+ "pytest-xdist >= 2.5.0",
+ "pylint >= 2.13.7",
+ "black >= 22.3.0",
+ "sphinx >= 4.5.0",
+]
+
+[project.urls]
 homepage = "https://github.com/MIT-LCP/wfdb-python/"
 repository = "https://github.com/MIT-LCP/wfdb-python/"
 documentation = "https://wfdb.readthedocs.io/"
-license = "MIT"
-
-[tool.poetry.dependencies]
-python = ">=3.7"
-numpy = ">=1.10.1,<2.0.0"
-scipy = ">=1.0.0"
-pandas = ">=1.3.0"
-SoundFile = ">=0.10.0"
-matplotlib = ">=3.2.2"
-requests = ">=2.8.1"
-pytest = {version = ">=7.1.1", optional = true}
-pytest-xdist = {version = ">=2.5.0", optional = true}
-pylint = {version = ">=2.13.7", optional = true}
-black = {version = ">=22.3.0", optional = true}
-Sphinx = {version = ">=4.5.0", optional = true}
-
-[tool.poetry.extras]
-dev = ["pytest", "pytest-xdist", "pylint", "black", "Sphinx"]
-
-# Do NOT use [tool.poetry.dev-dependencies]. See: https://github.com/python-poetry/poetry/issues/3514
 
 [tool.black]
 line-length = 80
 target-version = ['py37']
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+[tool.hatch.build.targets.sdist]
+exclude = [
+ "/tests",
+ "/sample-data",
+ "/demo-img.png",
+ "/demo.ipynb",
+]
+
+[tool.hatch.version]
+path = "wfdb/version.py"