Bump version to 1.9.2 #680

	name: Lint and run tests

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- '*'

	jobs:
	lint-and-run-tests:
	runs-on: ubuntu-latest
	permissions:
	contents: read
	strategy:
	matrix:
	python-version: [ "3.9", "3.10", "3.11", "3.12" ]

	steps:
	# For SonarCloud scan
	- uses: actions/checkout@v4
	if: matrix.python-version == '3.12'
	with:
	fetch-depth: 0

	- uses: actions/checkout@v4
	if: matrix.python-version != '3.12'

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	# for nextflow
	- name: Set up Java Runtime Environment
	uses: actions/setup-java@v4
	with:
	java-version: '21'
	distribution: 'temurin'

	- name: Install Nextflow 25.04.2 (standalone)
	run: \|
	curl -sL https://github.com/nextflow-io/nextflow/releases/download/v25.04.2/nextflow-25.04.2-dist -o nextflow
	chmod +x nextflow
	sudo mv nextflow /usr/local/bin/
	nextflow -version

	- name: Install deps
	run: \|
	python -m pip install --upgrade pip setuptools
	pip install poetry
	poetry install --all-extras

	- name: Run lint
	run: \|
	poetry run flake8 cirro

	- name: Run Tests
	run: \|
	poetry run pytest --cov --cov-report=xml --cov-branch -o junit_family=xunit2 --junitxml=junit/test-results.xml

	- name: SonarCloud Scan
	uses: sonarsource/sonarcloud-github-action@master
	if: matrix.python-version == '3.12' # Only run once
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

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