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Test

[pre-commit.ci] pre-commit autoupdate #183

	name: Test

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]
	schedule:
	- cron: "0 5 1,15 * *"

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

	jobs:
	test:
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -e {0} # -e to fail on error

	strategy:
	fail-fast: false
	matrix:
	include:
	- os: ubuntu-latest
	python: "3.10"
	- os: ubuntu-latest
	python: "3.11"
	- os: ubuntu-latest
	python: "3.11"
	pip-flags: "--pre"
	name: PRE-RELEASE DEPENDENCIES

	name: ${{ matrix.name }} Python ${{ matrix.python }}

	env:
	OS: ${{ matrix.os }}
	PYTHON: ${{ matrix.python }}

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python }}
	cache: "pip"
	cache-dependency-path: "**/pyproject.toml"

	- uses: actions/checkout@v4
	- name: Install R
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: "4"

	- name: Install edgeR
	run: Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='http://cran.us.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')"
	- name: Install test dependencies
	run: \|
	python -m pip install --upgrade pip wheel
	- name: Install dependencies
	run: \|
	pip install ${{ matrix.pip-flags }} ".[dev,test]"
	- name: Test
	env:
	MPLBACKEND: agg
	PLATFORM: ${{ matrix.os }}
	DISPLAY: :42
	run: \|
	coverage run -m pytest -v --color=yes
	- name: Report coverage
	run: \|
	coverage report
	- name: Upload coverage
	uses: codecov/codecov-action@v3

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