Improve MSA sorting and guard against None #40

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: CLI smoke test AF2

	on: [push]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11", "3.12", "3.13"]

	steps:
	- run: df -h
	- name: "node-cleanup"
	run: \|
	sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL
	sudo docker image prune --all --force
	sudo docker builder prune -a
	- run: df -h
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest pytest-cov
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	pip install -e .[af]
	- name: Test AF2
	run: \|
	set -x
	echo $(pwd)
	YUNTA_TEST=1 bash test/scripts/test-af2.sh gh

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