Merge remote-tracking branch 'origin/main' #246

	# This is a basic workflow to help you get started with Actions

	name: Testing

	# Controls when the workflow will run
	on:
	# Triggers the workflow on push or pull request events but only for the main branch
	push:
	branches:
	- main
	- dev
	pull_request:
	branches:
	- main
	- dev
	workflow_dispatch: # make is manually start-able

	# A workflow run is made up of one or more jobs that can run sequentially or in parallel
	jobs:
	# This workflow contains a single job called "test"
	test:
	# strategy:
	# matrix:
	# os: ['ubuntu-latest']
	# python-version: ['3.10']
	# include:
	# - os: 'macos-latest'
	# python-version: ['3.7', '3.8', '3.9', '3.11']
	# if: github.ref == 'refs/heads/main'
	# - python-version: ['3.7']
	# if: github.ref == 'refs/heads/dev'

	runs-on: 'ubuntu-latest'
	steps:
	- uses: actions/checkout@v3

	- name: Setup Mamba
	uses: conda-incubator/setup-miniconda@v2
	with:
	python-version: '3.10'
	miniforge-variant: Mambaforge
	miniforge-version: latest
	activate-environment: MPP
	use-mamba: true

	- name: Install environment
	shell: bash -l {0}
	run: \|
	mamba install -c conda-forge -c mosek -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt foldseek mmseqs2 cd-hit mash tmalign cvxpy pytest-cov rdkit pytest-cases scikit-learn mosek pyyaml
	pip install grakel

	- name: Run tests
	shell: bash -l {0}
	run: \|
	cd tests
	pytest -m "not todo and not issue" --cov=../datasail/ --cov-report=xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	fail_ci_if_error: false
	files: coverage.xml

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