Add NeuroMark #46

	name: continuous integration

	on:
	push:
	branches:
	- main
	tags:
	- "..*" # Any tag that looks like a version
	pull_request:
	branches:
	- main

	jobs:
	test:
	runs-on: self-hosted
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Setup container
	run: \|
	docker run \
	--detach \
	--rm \
	--name="build" \
	--volume="/home/runner:/home/runner" \
	--volume="$(pwd):/halfpipe" \
	--workdir="/halfpipe" \
	--entrypoint="tail" \
	${{ secrets.REGISTRY }}/halfpipe \
	--follow /dev/null

	- name: Install dependencies
	shell: docker exec build bash -x -e {0}
	run: \|
	apt-get --yes update
	apt-get --yes install libreoffice git zip

	- name: Build atlases
	id: build_atlases
	shell: docker exec build bash -x -e {0}
	run: \|
	cat > "${FREESURFER_HOME}/license.txt" <<EOF
	[email protected]
	73053
	*C8FMo8yrzcZA
	FSCA7.lDgNIow
	e1n3o06osRFD3qtBRgsTy9f9bQHGOpY/riIUrHoEx5c=
	EOF

	pip install --verbose .

	atlas_dir=atlases
	mkdir ${atlas_dir}
	pushd ${atlas_dir} \|\| exit

	halfpipe-atlases-build

	zip_path=atlases.zip
	zip ${zip_path} *

	echo "zip_path=${zip_path}" >> "${GITHUB_OUTPUT}"

	- name: Stop container
	run: \|
	docker kill build

	- name: Upload atlases
	uses: actions/upload-artifact@v4
	with:
	name: atlases.zip
	path: ${{ steps.build_atlases.outputs.zip_path }}

	- name: Release
	uses: softprops/action-gh-release@v2
	if: startsWith(github.ref, 'refs/tags/')
	with:
	files: ${{ steps.build_atlases.outputs.zip_path }}

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