Tests

Merge pull request #78 from vinisalazar/dev #403

# to view logs

	name: Tests

	on:
	push:
	branches:
	- main
	- dev

	jobs:
	formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository and submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	- name: Formatting
	uses: github/super-linter@v4
	env:
	VALIDATE_ALL_CODEBASE: true
	DEFAULT_BRANCH: main
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Install dependencies and lint
	run: \|
	pip install snakefmt
	pip install .
	python -m snakefmt metaphor/workflow/Snakefile

	run-workflow:
	runs-on: ubuntu-latest
	needs:
	- linting
	- formatting
	steps:
	- name: Checkout repository and submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	- name: Set up Python 3.9
	uses: actions/setup-python@v4
	with:
	python-version: 3.11
	# Deactivate this for now
	# - name: Install dependencies
	# run: \|
	# $CONDA/bin/conda env update --file environment.yaml --name base
	- name: Test workflow
	run: \|
	conda config --set channel_priority strict
	pip install .
	python -m metaphor.cli.cli test --dry-run

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