MIN Move SemiBin1 subcommands to bottom #413

	name: semibin_test

	on: [push, pull_request]

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest, windows-latest]
	python-version:
	- "3.7"
	- "3.8"
	- "3.9"
	- "3.10"
	- "3.11"

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: test
	python-version: ${{ matrix.python-version }}
	auto-activate-base: false
	- name: Install dependencies
	shell: bash -l {0}
	run : \|
	pip install pandas
	pip install numpy
	pip install .
	pip install pytest
	pip install hypothesis
	pip install python-igraph
	pip install torch
	pip install scikit-learn
	pip install requests
	pip install numexpr
	conda install -c bioconda bedtools hmmer fraggenescan samtools==1.6
	conda install -c bioconda prodigal
	conda install -c conda-forge -c bioconda mmseqs2=13.45111
	python ./setup.py install
	- name: Test with pytest
	shell: bash -l {0}
	run: \|
	python -m pytest ./test
	- name: Test with SemiBin command
	shell: bash -l {0}
	run: \|
	for t in integration-tests/*.py; do
	echo "Running $t ..."
	python $t
	done

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