fix notebook #22

	name: "[test] test siibra-paper notebooks"

	on:
	push:
	branches: ["main", "refactor_attr"]
	pull_request:
	branches: ["*"]

	jobs:
	test_tutorials:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.8

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -U .
	pip install matplotlib jupyter
	sudo apt-get install -y pandoc texlive-xetex

	- name: Run notebooks with nbmake
	run: \|
	error_flag=0
	for notebook in $(find ./paper_notebooks -type f)
	do
	echo "jupyter execute $notebook --allow-errors --inplace"
	jupyter execute $notebook --allow-errors --inplace

	# All error cells
	ERROR_CELLS=$(jq -r '[.cells[].outputs[] \| select( .output_type == "error" )]' $notebook)

	# Set error flag
	echo $ERROR_CELLS \| jq 'length'
	if [[ $(echo $ERROR_CELLS \| jq 'length') -gt "0" ]]
	then
	echo "Setting error flag."
	error_flag=1
	fi

	# Print error messages
	echo $ERROR_CELLS \| jq -rc '.[]' $notebook \
	\| while IFS= read -r line
	do
	echo $line \| jq -rc '.traceback \| join("")'
	done

	echo "jupyter nbconvert --to pdf $notebook"
	jupyter nbconvert --to pdf $notebook
	done

	if [[ ! $error_flag -eq "0" ]]
	then
	exit 1
	fi

	- if: always()
	name: Archive code coverage results
	uses: actions/upload-artifact@v4
	with:
	name: Notebook PDFs
	path: \|
	paper_notebooks/*.pdf
	paper_notebooks/*.ipynb

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