Ia/docs deploy ci #2

	name: Build and Deploy Docs
	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main
	jobs:
	build_docs:
	name: Build and Deploy Documentation
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	fetch-depth: 0 # to ensure other branches are available for build
	- name: Install system dependencies
	run: sudo apt-get install -y libhdf5-dev
	- name: Set r compilation options
	run: bash -c 'echo -e "MAKEFLAGS=--jobs=3\nCXXFLAGS += -O1 -UNDEBUG" > "$GITHUB_WORKSPACE/Makevars.user" && echo "R_MAKEVARS_USER=$GITHUB_WORKSPACE/Makevars.user" >> "$GITHUB_ENV"'
	- name: Setup R
	uses: r-lib/actions/setup-r@v2
	- name: Install R dependencies
	uses: r-lib/actions/setup-r-dependencies@v2
	with:
	cache-version: 1
	working-directory: 'r'
	extra-packages: 'pkgdown'
	- name: Create git worktree with docs branch
	run: git worktree add r/docs docs-html
	- name: Build documentation
	run: Rscript .github/workflows/deploy-reference.R
	- name: Create new branch
	run: \|
	git checkout -b update-docs-${{ github.sha }}
	git add .
	git commit -m "Update documentation for commit ${{ github.sha }}"
	working-directory: r/docs

	- name: Push changes to new branch
	run: git push origin update-docs-${{ github.sha }}
	- name: Create Pull Request
	uses: peter-evans/create-pull-request@v7
	with:
	token: ${{ secrets.GITHUB_TOKEN }}
	branch: update-docs-${{ github.sha }}
	base: docs-html
	title: "Update documentation for ${{ github.sha }}"
	body: "This PR updates the documentation site for commit ${{ github.sha }}."
	labels: documentation

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