Remove dev packages and run on bioconductor_docker #60

	name: pkgdown

	on:
	push:
	branches:
	- jomain

	# on:
	# repository_dispatch:
	# types: [trigger-workflow-2]

	jobs:
	build-and-deploy:
	runs-on: ubuntu-latest
	container: rformassspectrometry/metabonaut:latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	steps:
	- uses: actions/checkout@v4

	- name: Verify Quarto Installation
	run: quarto --version

	- name: Install rcmdcheck
	run: \|
	install.packages('rcmdcheck')
	shell: Rscript {0}

	- name: Check
	env:
	_R_CHECK_CRAN_INCOMING_REMOTE_: false
	run: \|
	Rscript -e "rcmdcheck::rcmdcheck(args = c('--no-manual'), error_on = 'error', check_dir = 'check')"
	shell: bash {0}

	- name: Install deploy dependencies
	run: \|
	apt-get update
	apt-get -y install rsync

	- name: Install pkgdown
	if: github.ref == 'refs/heads/main'
	run: \|
	install.packages('pkgdown')
	shell: Rscript {0}

	- name: Install package
	if: github.ref == 'refs/heads/main'
	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
	## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
	## at least one locally before this will work. This creates the gh-pages
	## branch (erasing anything you haven't version controlled!) and
	## makes the git history recognizable by pkgdown.

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