ci: change test env build triggering method #259



	name: code coverage

	on:
	push:
	branches: [ "dev" ]
	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@v4
	with:
	ref: dev

	- 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
	install-pandoc: false
	extra-packages: \|
	any::rcmdcheck
	any::testthat
	any::covr
	any::RColorBrewer
	any::reticulate
	any::Matrix
	any::future
	any::BiocParallel
	any::remotes
	needs: coverage

	- uses: actions/setup-python@v5
	with:
	python-version: "3.x"

	- name: setup r-reticulate venv
	shell: Rscript {0}
	run: \|
	path_to_python <- reticulate::virtualenv_create(
	envname = "r-reticulate",
	python = Sys.which("python"), # placed on PATH by the setup-python action
	packages = c(
	"scipy"
	)
	)

	writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
	Sys.getenv("GITHUB_ENV"))

	- 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@v4
	with:
	token: d7b84f7b-f2a9-46ed-9ef8-6165425e259f
	fail_ci_if_error: false
	flags: unittests
	verbose: true

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