test

Update to match neurodatascience/nipoppy:main #152

	---
	name: test

	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

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

	steps:

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

	- uses: actions/setup-python@v4
	with:
	python-version: '3.11'

	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y git-annex

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

	- name: Install data
	run: make -C tests data/ds004097

	- name: Test
	run: python -m pytest tests --cov-report=xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	file: ./coverage.xml
	name: codecov-umbrella
	fail_ci_if_error: false

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