feat: METHYLVI retrieve normalized methylation levels for specific context #2086

	name: test

	on:
	push:
	branches: [main, "[0-9]+.[0-9]+.x"]
	pull_request:
	schedule:
	- cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
	workflow_dispatch:

	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:
	os: [ubuntu-latest]
	python: ["3.10", "3.11", "3.12"]

	name: integration

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

	steps:
	- uses: actions/checkout@v4

	- uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python }}
	cache: "pip"
	cache-dependency-path: "**/pyproject.toml"

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip wheel uv
	python -m uv pip install --system "scvi-tools[tests] @ ."

	- name: Run pytest
	env:
	MPLBACKEND: agg
	PLATFORM: ${{ matrix.os }}
	DISPLAY: :42
	COLUMNS: 120
	run: \|
	coverage run -m pytest -v --color=yes
	coverage report

	- uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

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