Edits to renderRMarkdown.yaml to hopefully fix auth issues #86

	# Github action that renders R markdown when PR is opened
	# All R markdown is run in container/rmd.Dockerfile

	on:
	pull_request:
	types: [opened, reopened, edited]
	push:
	workflow_dispatch:

	name: render-rmarkdown

	jobs:
	render-rmarkdown:
	runs-on: ubuntu-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Build and push Docker image
	uses: docker/build-push-action@v5
	with:
	file: container/rmd.Dockerfile
	context: .
	push: false # Set to true if you want to push the image to a registry
	tags: notebook-runner
	cache-from: type=gha
	cache-to: type=gha,mode=max

	- name: Run Docker container to compile assets
	uses: addnab/docker-run-action@v3
	with:
	image: notebook-runner
	options: -v ${{ github.workspace }}:/workspace --rm -u root
	run: \|
	RMD_FILES=$( find /workspace -name "Rmd" -o -name "rmd" )
	if [ -n "$RMD_FILES" ]; then
	echo $RMD_FILES
	for RMD in $RMD_FILES
	do
	Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f, output_format = "all")' $RMD
	done
	else
	echo "No R markdown found. Skipping execution."
	fi
	#Checkout again to avoid race condition with parallel-running Jupyter rendering script.
	- uses: actions/checkout@v4
	- uses: stefanzweifel/git-auto-commit-action@v5

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