Migrate from `poetry` to `uv` #216

	name: ci

	on:
	push:
	tags:
	- v*
	pull_request:
	branches: [main]

	jobs:
	pre-commit:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v3
	- uses: pre-commit/action@v3.0.1

	tests:
	needs: [pre-commit]
	name: "pytest and snakemake"
	runs-on: ubuntu-latest

	strategy:
	matrix:
	python-version: ["3.10", "3.11", "3.12"]

	steps:
	- uses: actions/checkout@v4

	- name: Set up the environment
	uses: ./.github/actions/setup-python-env
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install extra dependencies
	run: uv sync --extra cellpose --extra wsi --dev && uv run pip install snakemake 'pulp<2.8'

	- name: Tests
	run: uv run pytest

	- name: Snakemake
	run: cd workflow && uv run snakemake --config sdata_path=tuto.zarr --configfile=config/toy/cellpose.yaml --workflow-profile profile/ci -c1

	deploy-docs:
	needs: [tests]
	if: contains(github.ref, 'tags')
	name: "Deploy documentation"
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up the environment
	uses: ./.github/actions/setup-python-env

	- name: Build documentation
	run: uv run mkdocs gh-deploy --force

	pypi-release:
	needs: [tests]
	if: contains(github.ref, 'tags')
	name: "PyPI release"
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4

	- name: Set up the environment
	uses: ./.github/actions/setup-python-env

	- name: Build
	run: uv build

	- name: Publish
	run: uv publish -t ${{ secrets.PYPI_TOKEN }}

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