Test Coverage #282

	# 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
	name: Test Coverage

	on:
	push:
	branches: main
	paths-ignore:
	- ".github/**"
	- ".devcontainer/**"
	workflow_run:
	workflows: "R-CMD-check"
	types: completed
	workflow_dispatch:

	concurrency:
	group: ${{ github.workflow }}
	cancel-in-progress: true

	jobs:
	test-coverage:
	runs-on: ubuntu-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	BCFTOOLS_VERSION: 1.15.1

	steps:
	- uses: actions/checkout@v4

	- uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true

	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: any::covr, local::.
	needs: coverage

	- name: Install BCFtools
	if: runner.os == 'Linux'
	run: \|
	sudo apt-get update && \
	sudo apt-get install -y --no-install-recommends \
	libxt6 \
	ca-certificates \
	bzip2 \
	wget \
	autoconf \
	automake \
	make \
	cmake \
	libbz2-dev \
	liblzma-dev \
	libjpeg-dev \
	libxml2-dev \
	zlib1g-dev \
	libgdal-dev
	wget -q -P /tmp/ https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
	tar -C /tmp/ -xjf /tmp/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
	cd /tmp/bcftools-${BCFTOOLS_VERSION} && \
	sudo autoreconf -i && \
	sudo ./configure --prefix=/usr && \
	sudo make && \
	sudo make install

	- name: Test coverage
	run: covr::codecov(quiet = FALSE)
	shell: Rscript {0}

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