Refactor workflow to use satijalab/seurat-ci image #13

	name: Integration Checks

	# Because `main` is a protected branch this workflow is triggered when a PR
	# is opened/updated and again when it is merged.
	on:
	push:
	branches:
	- main
	- testing-ci
	pull_request:
	branches:
	- main

	jobs:
	check-package:
	runs-on: ubuntu-latest

	# Use the `satijalab/seurat-ci` Docker image as the container environment.
	# This image is pre-configured with everything required for running
	# integration checks, for more details, see
	# https://hub.docker.com/repository/docker/satijalab/seurat-ci/general.
	container:
	image: satijalab/seurat-ci:latest

	steps:
	# Pull the latest changes from the repository down to the runner.
	- name: Checkout
	uses: actions/checkout@v4

	# Install the package and _all_ its dependencies.
	- name: Install Dependencies
	run: installAllDeps.r

	# Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails
	# and the output of `rcmdcheck` will be uploaded as an artifact.
	- name: Run Checks
	run: \|
	rcmdcheck::rcmdcheck(
	args = c("--no-manual", "--as-cran"),
	build_args="--no-manual",
	error_on="warning"
	)
	shell: Rscript {0}
	continue-on-error: true

	# Build the pkgdown site.
	- name: Build Website
	run: \|
	pkgdown::build_site_github_pages(
	new_process = FALSE,
	install = FALSE
	)
	shell: Rscript {0}

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