Trying to output stdout using -u #5

	name: Run Notebooks and Save Outputs

	on:
	push:
	branches:
	- main # Trigger the action on the main branch

	jobs:
	run-notebooks:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v3

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

	- name: Install dependencies
	run: \|
	pip install -r requirements.txt

	- name: Verify Installation and PATH
	run: \|
	pip list
	echo $PATH
	which openneuro-py

	- name: Run Jupyter Notebooks
	run: \|
	mkdir -p executed_notebooks
	for notebook in $(find . -name "*.ipynb"); do
	echo "Executing $notebook"
	python -u -m jupyter nbconvert --to notebook --execute --inplace \
	--ExecutePreprocessor.timeout=600 \
	--output executed_notebooks/$(basename $notebook) $notebook \
	\|\| exit 1
	done

	- name: Commit and Push Notebooks with Outputs
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "GitHub Action"
	git checkout -b with-outputs \|\| git checkout with-outputs
	cp -r executed_notebooks/* .
	git add *.ipynb
	git commit -m "Add notebooks with outputs"
	git push --force origin with-outputs

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