Merge pull request #754 from josschavezf/suite_modular #3



	name: code coverage

	on:
	push:
	branches: [ "suite_modular" ]
	# pull_request:
	# types: closed
	# branches: [ "main" ]
	schedule:
	- cron: '16 20 * * 2'

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

	steps:

	- name: Checkout repo for workflow access
	uses: actions/checkout@v3

	- name: Set up R environment
	uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true

	- name: Set up dependencies (general)
	uses: r-lib/actions/setup-r-dependencies@v2
	env:
	_R_CHECK_FORCE_SUGGESTS: false
	_R_CHECK_RD_XREFS: false
	with:
	dependencies: '"hard"' # do not use suggested dependencies
	extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
	needs: coverage

	- name: Set up dependencies (GiottoData)
	run: \|
	suppressWarnings({
	remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
	})
	shell: Rscript {0}

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

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: e6770448-c694-49d7-b83f-b6cb21c0e7ad
	fail_ci_if_error: false
	flags: unittests
	verbose: true

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