pkgdown #146

	# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
	# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
	on:
	workflow_run:
	workflows: [R-CMD-check]
	types: [completed]
	push:
	branches: [dev]

	name: pkgdown

	env:
	PKGDOWN_DEV_MODE: ${{ github.ref == 'refs/heads/dev' && 'devel' \|\| 'default' }}

	jobs:
	pkgdown:
	runs-on: ubuntu-24.04
	# Only restrict concurrency for non-PR jobs
	concurrency:
	group: pkgdown-${{ github.event_name != 'pull_request' \|\| github.run_id }}
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	permissions:
	contents: write
	steps:
	- uses: actions/checkout@v3

	- uses: r-lib/actions/setup-pandoc@v2

	- uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true

	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: any::pkgdown
	needs: website

	- name: Check dev mode
	run: echo "$GITHUB_ENV"

	- name: Install htslib
	run: \|
	sudo apt-get update
	sudo apt-get install -y libhts-dev
	echo "-------------------HTSLIB-----------------------"
	pkg-config --cflags --libs htslib
	echo "------------------------------------------------"

	- name: Install iscream
	run: R CMD INSTALL .

	- name: Build site
	run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
	shell: Rscript {0}

	- name: Deploy to GitHub pages 🚀
	if: github.event_name != 'pull_request'
	uses: JamesIves/[email protected]
	with:
	clean: false
	branch: gh-pages
	folder: docs

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