merged unitig bam #16

	# 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: Python application

	on:
	push:
	branches: [ "refactoring" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.10
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"
	- name: Conda installation
	run: \|
	mkdir -p ~/miniconda3
	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
	bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
	rm -rf ~/miniconda3/miniconda.sh
	~/miniconda3/bin/conda init bash
	~/miniconda3/bin/conda init zsh
	- name: Strainy Install
	run: \|
	#cd strainy
	ls
	git submodule update --init
	make -C submodules/Flye
	conda env create -f environment.yml -n strainy
	- name: Test strainy
	run: \|
	conda run -n strainy ./strainy.py --gfa test_set/toy.gfa --fastq test_set/toy.fastq.gz --output out_strainy --mode hifi --threads 16
	- name: Check gfa
	run: \|
	pip install -U pytest
	pip install gfapy
	pytest test_set/toy.py

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