Refactor multihypothesis segmentation handling #115

	name: Test

	on:
	push:
	branches:
	- main
	pull_request:

	jobs:
	ruff:
	name: Ruff
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: chartboost/ruff-action@v1
	with:
	args: 'format --check'

	test:
	name: Test
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11"]

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install conda dependencies
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	environment-file: conda_config.yml
	channel-priority: true
	- name: Install pip dependencies
	shell: bash -el {0} # this is necessary to activate the conda env
	run: \|
	pip install ".[dev]"
	- name: Test with pytest
	shell: bash -el {0}
	run: \|
	pytest --color=yes --cov=motile_toolbox --cov-report=xml --cov-report=term-missing tests
	# Coverage should work out of the box for public repos. For private repos, more setup is likely required.
	- name: Coverage
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	slug: funkelab/motile_toolbox

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