check

New skeleton structure adapted from Nextflow/Python repository #6

	name: check

	on:
	push:
	branches:
	- main
	pull_request:

	jobs:
	toolkit:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- uses: mamba-org/setup-micromamba@v1
	with:
	micromamba-version: '1.5.6-0'
	environment-name: test
	environment-file: dependencies/dev.yml
	cache-environment: true
	post-cleanup: 'all'
	- name: Install Poetry
	uses: snok/install-poetry@v1
	- name: Install toolkit
	shell: micromamba-shell {0}
	run: \|
	cd toolkit
	poetry install
	- name: Run style checks and unit tests
	shell: micromamba-shell {0}
	run: \|
	bash scripts/check.sh

	workflow:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Build Docker images
	run: \|
	bash scripts/docker.sh
	- uses: mamba-org/setup-micromamba@v1
	with:
	micromamba-version: '1.5.6-0'
	environment-name: test
	environment-file: dependencies/dev.yml
	cache-environment: true
	post-cleanup: 'all'
	- name: Run workflow
	shell: micromamba-shell {0}
	env:
	PROFILES: local,test,linux
	run: \|
	pytest --git-aware tests/integration/

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