Setup CD pipeline for rawrassembly #58

	# This workflow uses actions that are not certified by GitHub.
	# They are provided by a third-party and are governed by
	# separate terms of service, privacy policy, and support
	# documentation.
	#
	# See https://github.com/r-lib/actions/tree/master/examples#readme for
	# additional example workflows available for the R community.

	name: R-CMD-check-rawrr
	env:
	ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
	on:
	push:
	branches: [ devel ]
	pull_request:
	branches: [ devel ]
	workflow_dispatch:

	jobs:
	build:
	runs-on: ubuntu-20.04
	strategy:
	matrix:
	r-version: [4.3]
	steps:
	- uses: actions/checkout@v4
	- name: Set up R ${{ matrix.r-version }}
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: ${{ matrix.r-version }}
	- name: Install Linux packages
	run: sudo apt-get install -y mono-mcs mono-xbuild libcurl4-openssl-dev libicu-dev pandoc pandoc-citeproc texlive texlive-latex-extra texlive-fonts-extra
	shell: bash {0}
	- name: Install dependencies
	run: \|
	install.packages(c("remotes", "covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "BiocManager"))
	BiocManager::install(c("BiocStyle", "ExperimentHub", "tartar"))
	remotes::install_deps(dependencies = TRUE)
	shell: Rscript {0}
	- name: Check
	run: rcmdcheck::rcmdcheck(build_args = "", args = "", error_on = "error", check_dir = "/tmp/rawrr.Rcheck")
	shell: Rscript {0}
	- name: codecov
	run: covr::codecov(type = "all",token=Sys.getenv('CODECOV_TOKEN'))
	shell: Rscript {0}
	- uses: actions/upload-artifact@v4
	with:
	name: rawrr.Rcheck
	path: /tmp/rawrr.Rcheck
	if-no-files-found: warn

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