re-install monocle3 and cicero #145

	# 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:
	push:
	branches: [main, master, dev_SeuratV5]
	pull_request:
	branches: [main, master, dev_SeuratV5]
	release:
	types: [published]
	workflow_dispatch:

	name: pkgdown

	jobs:
	pkgdown:
	runs-on: ubuntu-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	steps:
	- uses: actions/checkout@v2

	- 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, any::reticulate, local::., any::devtools
	needs: website

	- uses: actions/setup-python@v2
	with:
	python-version: '3.10'

	- name: Setup hummuspy env
	run: \|
	reticulate::conda_create("r-reticulate", packages="python==3.10")
	reticulate::py_install("hummuspy", envname = "r-reticulate", pip=TRUE)
	shell: Rscript {0}

	- name: ubuntu setup for Monocle3
	run: sudo apt-get install libgdal-dev libgeos-dev libproj-dev

	- name: Install Monocle3
	run: devtools::install_github('cole-trapnell-lab/monocle3')
	shell: Rscript {0}

	- name: Install Cicero
	run: devtools::install_github("cole-trapnell-lab/cicero-release", ref = "monocle3")
	shell: Rscript {0}

	- 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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