Merge pull request #66 from adrientaudiere/master #55

	# 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:
	pull_request:
	branches: [main, master]

	name: test-coverage

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

	steps:
	- uses: actions/checkout@v3

	- 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
	needs: coverage

	- name: Install vsearch
	run: sudo apt-get install vsearch

	- name: Install blastn
	run: sudo apt-get install ncbi-blast+

	- name: Install mumu
	run: \|
	git clone https://github.com/frederic-mahe/mumu.git \
	&& cd ./mumu/ \
	&& make \
	&& make check \
	&& sudo make install

	- name: Test coverage
	run: \|
	covr::codecov(
	quiet = FALSE,
	clean = FALSE,
	install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
	)
	shell: Rscript {0}

	- name: Show testthat output
	if: always()
	run: \|
	## --------------------------------------------------------------------
	find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; \|\| true
	shell: bash

	- name: Upload test results
	if: failure()
	uses: actions/upload-artifact@v3
	with:
	name: coverage-test-failures
	path: ${{ runner.temp }}/package

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