Revamp CI checks #2

	name: Integration Checks

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

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

	# Use the `satijalab/seurat-ci` Docker image as the runner 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 using scripts from
	# `littler`, see https://eddelbuettel.github.io/littler/ for details.
	- name: Install Dependencies
	run: installDeps.r -s

	# A significant number of `Seurat`'s tests are skipped during CRAN checks
	# so we'll run the tests separately.
	- name: Run Tests
	run: testthat::test_local()
	shell: Rscript {0}
	continue-on-error: true

	# Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails.
	# Avoid re-running tests redundantly.
	- name: Run CRAN Checks (no tests)
	run: \|
	rcmdcheck::rcmdcheck(
	args = c("--as-cran", "--no-tests"),
	error_on="warning"
	)
	shell: Rscript {0}
	continue-on-error: true

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