(WIP)Added analyze_selection_criteria.ipynb and edit ems_training notebook #114

	name: Rebuild website and manuscript

	on:
	pull_request_target:
	types: [closed]
	paths:
	- 'code/*/.ipynb'
	- 'website/**'

	jobs:
	build_website:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false

	steps:
	- name: Checkout repository
	uses: actions/checkout@v6
	with:
	token: ${{ secrets.CI_TOKEN }}
	fetch-depth: 0

	- name: Setup pixi
	uses: prefix-dev/[email protected]
	with:
	run-install: false

	- name: Build website and manuscript
	shell: pixi exec --spec coreutils --spec findutils --spec ghp-import --spec grep --spec jupyter-book --spec nbconvert-core --spec rsync -- bash -e {0}
	run: \|
	# Build website
	rm -f pipeline/*.ipynb
	jupyter-book build . --path-output . --config website/_config.yml --toc website/_toc.yml
	rsync -auzP code/images/* _build/html/_images/
	ghp-import -n -p -f _build/html

	# Link notebooks
	find code -name '*.ipynb' \| grep -v "ipynb_checkpoints" \| xargs -I % bash -c 'ln -s ../% pipeline/$(basename %)'

	# Make manuscript
	cd website/nature_protocol
	jupyter nbconvert --to notebook --execute conversion_notebook.ipynb && rm -f conversion_notebook.nbconvert.ipynb

	- name: Commit changes to pipeline
	uses: EndBug/add-and-commit@v9
	with:
	push: true
	message: Update pipeline

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