Tests

Add support for error-free reads with --errfree argument and separate BAM file processing #55

	name: Tests

	on:
	push:
	branches:
	- main
	paths:
	- ".github/workflows/unit-tests.yml"
	- "tests/**"
	- "mess/**"
	- "setup.py"
	- "!.github/workflows/build-docs.yml"
	- "!docs/**"
	- "!mkdocs.yml"
	- "!README.md"
	pull_request:
	paths:
	- ".github/workflows/unit-tests.yml"
	- "tests/**"
	- "mess/**"
	- "setup.py"
	- "!.github/workflows/build-docs.yml"
	- "!docs/**"
	- "!mkdocs.yml"
	- "!README.md"

	permissions:
	contents: read

	jobs:
	tests:
	name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
	runs-on: ${{ matrix.os }}

	defaults:
	run:
	shell: bash -el {0}

	strategy:
	matrix:
	os: [ubuntu-latest]
	python-version: ["3.12"]

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Setup MeSS environment
	uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-version: latest
	activate-environment: mess
	python-version: ${{ matrix.python-version }}
	auto-update-conda: true

	- name: Setup apt dependencies
	run: \|
	sudo add-apt-repository -y ppa:apptainer/ppa
	sudo apt-get update
	sudo apt install -y squashfuse fuse2fs gocryptfs apptainer

	- name: Disable apparmor namespace restrictions for apptainer
	run: \|
	sudo sh -c 'echo kernel.apparmor_restrict_unprivileged_userns=0 \
	>/etc/sysctl.d/90-disable-userns-restrictions.conf'
	sudo sysctl -p /etc/sysctl.d/90-disable-userns-restrictions.conf

	- name: Install MeSS and pytest-cov
	run: \|
	pip install -e .
	pip install pytest coverage

	- name: Run tests on ${{ matrix.os }} for python ${{ matrix.python-version }}
	run: \|
	coverage run -m pytest

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