Run tests #226

	---
	name: Run tests

	on:
	push:
	branches: ['*']
	pull_request:
	branches: ['*']
	schedule:
	- cron: '0 11 * * *' # Every day at 11:00 UTC
	workflow_dispatch:

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

	jobs:

	test:

	runs-on: ubuntu-latest

	strategy:
	matrix:
	# NOTE: when adding a new version, update the 'if' condition in
	# the 'Run API tests' step
	python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]

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

	steps:

	- uses: actions/checkout@v5
	with:
	submodules: recursive

	- uses: actions/setup-python@v6
	with:
	python-version: ${{ matrix.python-version }}
	allow-prereleases: true

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

	- name: Run non-API tests
	run: \|
	python -m pytest -m "not api and no_xdist" -n 0 --cov=nipoppy --cov-report=xml
	python -m pytest -m "not api and not no_xdist" --cov=nipoppy --cov-report=xml --cov-append

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v5
	with:
	files: ./coverage.xml
	name: codecov-umbrella
	token: ${{ secrets.CODECOV_TOKEN }}

	- name: Run API tests
	if: (github.event_name == 'schedule' \|\| github.event_name == 'workflow_dispatch') && matrix.python-version == '3.14'
	run: \|
	python -m pytest -m api
	env:
	ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }}
	ZENODO_ID: ${{ vars.ZENODO_ID }}

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