Bump actions/setup-python from 4 to 5 (#9) #145

	name: Run notebooks

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]
	schedule:
	- cron: "0 6 * * 1"

	jobs:
	run-notebooks:
	strategy:
	matrix:
	nb: [
	{title: quickstart, name: TorchIO_tutorial},
	{title: "brain parcellation", name: Brain_parcellation_with_TorchIO_and_HighRes3DNet},
	{title: transforms, name: Data_preprocessing_and_augmentation_using_TorchIO_a_tutorial},
	{title: frameworks, name: TorchIO_MONAI_PyTorch_Lightning},
	]
	fail-fast: false

	runs-on: ubuntu-latest

	steps:
	- name: Set up python
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"

	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Install dependencies
	run: \|
	pip install ipython ipykernel papermill
	ipython kernel install --name "python3" --user

	- name: Decrease RAM usage
	run: \|
	PARC_NB="notebooks/Brain_parcellation_with_TorchIO_and_HighRes3DNet.ipynb"
	sed -i 's/tio.Crop((0, 0, 10, 30, 40, 40))/tio.Crop((60, 60, 90, 110, 100, 100))/g' $PARC_NB
	sed -i 's/patch_size = 128/patch_size = 32/g' $PARC_NB

	- name: Run ${{ matrix.nb.title }} notebook
	run: \|
	IN_PATH=notebooks/${{ matrix.nb.name }}.ipynb
	OUT_PATH=${{ matrix.nb.name }}_output.ipynb
	papermill \
	--no-progress-bar \
	--log-output \
	$IN_PATH $OUT_PATH

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