Merge branch 'nipoppy:main' into bagel_update #1

	---
	name: Run tests

	on:
	push:
	branches: ['*']
	pull_request:
	branches: ['*']

	# cancel previous runs if new one is triggered
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:

	test:

	runs-on: ubuntu-latest

	strategy:
	matrix:
	python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

	# only trigger on upstream repo
	if: github.repository_owner == 'nipoppy' && github.event.repository.name == 'nipoppy'

	steps:

	- uses: actions/checkout@v3
	with:
	submodules: recursive

	- uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	allow-prereleases: true

	- name: Install package
	run: \|
	pip install -U pip
	pip install .[tests]

	- name: Run tests
	run: \|
	python -m pytest --cov=nipoppy --cov-report=xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	file: ./coverage.xml
	name: codecov-umbrella
	token: ${{ secrets.CODECOV_TOKEN }}

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