Guide Notebooks Regression #13

	name: Guide Notebooks Regression
	run-name: Guide Notebooks Regression
	on: [push]
	jobs:
	start_node_runner:
	runs-on: [self-hosted, nobrainer-self-hosted-ci]
	outputs:
	jobid: ${{ steps.sbatch.outputs.jobid }}
	steps:
	- name: sbatch
	id: sbatch
	run: \|
	jobid=$(sbatch \
	-t 100 \
	--mem 16G \
	-p gablab \
	-D ${HOME}/sw/actions-runner \
	run.sh \| cut -d ' ' -f 4)
	echo "Submitted batch job with id ${jobid}"
	echo "Waiting for job to start"
	while [ 1 ]; do
	node=$(squeue --noheader -j ${jobid} -o "%N")
	echo "Found node ${node}"
	if [ -z ${node} ]; then
	sleep 1;
	else
	break;
	fi
	done
	echo "jobid=${jobid}" >> "$GITHUB_OUTPUT"

	guide_notebooks_regression:
	needs: start_node_runner
	runs-on: [self-hosted, nobrainer-ci-self-hosted-runner]
	steps:
	- name: clone
	uses: actions/checkout@v3
	- name: install
	run: \|
	cd ${{ github.workspace }}
	python -m venv env
	source env/bin/activate
	pip install --upgrade pip
	pip install jupyter
	pip install -e .
	nobrainer info
	- name: run
	run: \|
	cd ${{ github.workspace }}
	for notebook in $(ls guide/[0-9][0-9]-*.ipynb); do
	echo "running ${notebook} from ${PWD}"
	echo $(ls {$PWD})
	singularity exec \
	--nv \
	-B /om \
	${HOME}/img/tensorflow_latest-gpu.sif \
	bash ${PWD}/run-in-env.sh \
	jupyter nbconvert \
	--execute ${PWD}/${notebook} \
	--to markdown \
	--stdout
	done

	shutdown_node_runner:
	if: always()
	needs: [start_node_runner, guide_notebooks_regression]
	runs-on: [self-hosted, nobrainer-self-hosted-ci]
	steps:
	- name: cleanup
	env:
	jobid: ${{ needs.start_node_runner.outputs.jobid }}
	run: \|
	echo "jobid is ${jobid}"
	scancel ${jobid}

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