chore(main): release 0.2.0 #269

	name: CI

	on:
	push:
	branches:
	- main
	pull_request:

	jobs:
	cancel-previous:
	runs-on: ubuntu-latest
	if: github.ref != 'refs/heads/main'
	steps:
	- uses: khan/pull-request-workflow-cancel@1.0.1
	with:
	workflows: "main.yml"
	env:
	GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'

	formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Install dependencies
	run: \|
	sudo apt-get install -y \
	liblzma-dev

	- uses: actions/checkout@v5

	- name: Install pixi
	uses: prefix-dev/setup-pixi@v0.8.1

	- name: Run Lint
	run: \|
	pixi run -e dev check

	# - name: Run Type Checks
	# run: \|
	# pixi run -e dev typecheck

	testing:
	runs-on: ubuntu-latest
	needs: formatting
	steps:
	- uses: actions/checkout@v5
	with:
	lfs: true

	- name: Install pixi
	uses: prefix-dev/setup-pixi@v0.8.1

	- name: Run tests
	run: \|
	pixi run -e dev test

	- name: Run MUC1 example as smoke text
	run: \|
	set -x

	mkdir -p /tmp/workdir/result
	pixi run \
	svirlpool run \
	--threads 1 \
	--samplename muc1test \
	--workdir /tmp/workdir/result \
	--alignments examples/muc1/data/muc1.bam \
	--reference examples/muc1/data/muc1.fa \
	--trf examples/muc1/data/muc1.trf.bed \
	--mononucleotides examples/muc1/data/muc1.mononucleotides.lt6.bed \
	--lamassemble-mat data/lamassemble-mats/promethion.mat
	pixi run \
	svirlpool sv-calling \
	--threads 1 \
	--reference examples/muc1/data/muc1.fa \
	--input /tmp/workdir/result/svirltile.db \
	--output /tmp/workdir/result/variants.vcf.gz

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