Add github action to knit Rmd #12

	name: Knit Rmd Files

	on:
	push:
	branches:
	- main
	pull_request:
	workflow_dispatch:

	jobs:
	knit:
	runs-on: ubuntu-latest
	permissions:
	contents: write
	pull-requests: write

	steps:
	- name: Setup pandoc
	uses: r-lib/actions/setup-pandoc@v2

	- name: Checkout repository
	uses: actions/checkout@v4
	# Only pull current branch, not the merge outcome so that we can commit the output
	with:
	ref: ${{ github.head_ref \|\| github.ref_name }}
	fetch-depth: 0

	- name: Set up R
	uses: r-lib/actions/setup-r@v2

	- name: Setup Renv
	uses: r-lib/actions/setup-renv@v2
	env:
	GITHUB_PAT: ${{ secrets.READ_OMOPCEPT_PAT }}

	- name: Tmp install omopcept in rmd # doesnt install on local because of arrow error
	run: \|
	Rscript -e '
	remotes::install_github("SAFEHR-data/omopcept")
	renv::snapshot()
	'
	env:
	GITHUB_PAT: ${{ secrets.READ_OMOPCEPT_PAT }}

	- name: Find and knit Rmd files
	run: \|
	Rscript -e '
	rmd_files <- list.files(pattern = "\\.Rmd$", recursive = TRUE)
	for (file in rmd_files) {
	rmarkdown::render(file)
	}
	'

	- name: Commit changes
	run: \|
	git config --global user.name "github-actions[bot]"
	git config --global user.email "github-actions[bot]@users.noreply.github.com"
	git add -A
	git commit -m "Knit Rmd files" \|\| echo "No changes to commit"

	- name: Push changes
	uses: ad-m/[email protected]
	with:
	branch: ${{ github.head_ref \|\| github.ref_name }}

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