Support for compiling FreeSurfer from source #270

	name: CI

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	on:
	pull_request:
	branches: [ master ]

	jobs:
	run-tests:
	runs-on: ubuntu-22.04
	strategy:
	matrix:
	python-version: ['3.11', '3.10', '3.9', '3.8']
	fail-fast: false
	steps:
	- name: Install Apptainer
	env:
	VERSION: 1.1.5
	run: \|
	sudo apt-get update
	sudo apt-get install -y wget
	wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer_${VERSION}_amd64.deb
	wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-suid_${VERSION}_amd64.deb
	sudo apt-get install --yes ./apptainer*
	- name: Set Apptainer/Singularity environment variables
	run: \|
	# Give reproenv the full path to apptainer, so it still works with `sudo`.
	echo REPROENV_APPTAINER_PROGRAM=apptainer >> $GITHUB_ENV
	echo APPTAINER_CACHEDIR=/dev/shm/$(whoami)/singularity >> $GITHUB_ENV
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install neurodocker
	run: python -m pip install --editable .[dev]
	- name: Run python tests
	run: pytest --numprocesses auto
	- name: Get code coverage
	run: codecov

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