Misc cleanup #1

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

	name: Command line interface tests

	on:
	push:
	branches: [ "master" ]
	pull_request:
	branches: [ "master" ]
	workflow_dispatch:
	inputs:

	permissions:
	contents: read

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.11"]

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v3
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip' # caching pip dependencies
	cache-dependency-path: '**/pyproject.toml'
	- name: Download fixtures
	run: \|
	wget https://www.dropbox.com/scl/fi/ivsqbao9we1lnyyyh43cc/ci_data.zip\?rlkey\=b9lcqxs63iv2409q5a7q1oh9z\&dl\=0 -O ci_data.zip
	unzip ci_data.zip
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest
	pip install -e .
	- name: Run VAMB
	run: \|
	vamb --outdir outdir_vamb --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz -l 32 -e 10 -q 2 -o C --minfasta 200000
	ls -la outdir_vamb
	cat outdir_vamb/log.txt
	- name: Run TaxVAMB
	run: \|
	vamb --model vaevae --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -e 10 -q 2 -o C --minfasta 200000
	ls -la outdir_taxvamb
	cat outdir_taxvamb/log.txt

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