Fix issue with empty proteomes by searching them on UniParc. #194

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: Python package

	on:
	push:
	branches: [ main ]
	paths-ignore:
	- 'article_data/**'
	- 'README.md'
	- 'CHANGELOG.md'
	- 'CONTRIBUTORS.md'
	- 'LICENSE'
	- 'tutorials/**'
	- 'pictures/**'
	pull_request:
	branches: [ main ]
	paths-ignore:
	- 'article_data/**'
	- 'README.md'
	- 'CHANGELOG.md'
	- 'CONTRIBUTORS.md'
	- 'LICENSE'
	- 'tutorials/**'
	- 'pictures/**'

	jobs:
	build:
	strategy:
	matrix:
	platform: [ubuntu-latest]
	python-version: [3.11]
	runs-on: ${{ matrix.platform }}
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Path to brew
	run: \|
	echo "/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin" >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	brew update
	brew install mmseqs2
	mmseqs -h
	pip install -e . --config-settings editable_mode=compat
	pip install datapane plotly ontosunburst kaleido numpy==1.26.4
	- name: Test with pytest
	run: \|
	pip install pytest pytest-mock
	cd test
	pytest test_proteomes.py
	pytest test_clustering.py
	pytest test_annotation.py
	pytest test_workflow.py
	pytest test_precomputed.py
	pytest test_eggnog.py
	pytest test_report.py

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