[Sync] Reorganize output directories + deduplicate snakefiles + bugfixes #8

	name: lint

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	lint:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Install Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.9"

	# TODO (KC): these pinned deps are copied from the dev env (cartograpy_dev.yml)
	- name: Install test dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install pre-commit==3.5.0 ruff==0.1.6 snakefmt==0.8.5

	- name: Run Ruff
	run: ruff check --output-format=github .

	- name: Run Ruff formatter
	run: ruff format --check .

	- name: Run Snakefmt
	run: snakefmt --check .

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