Add pre-commit hooks and linting action #132

	name: test-build

	on: pull_request

	jobs:
	run-workflow:
	runs-on: ubuntu-latest
	steps:

	- name: Checkout repository
	uses: actions/checkout@v2

	- id: auth
	name: Set up Google Cloud authentication
	uses: google-github-actions/auth@v2
	with:
	credentials_json: ${{ secrets.GOOGLE_CREDENTIALS }}

	- name: Set up Google Cloud SDK
	uses: google-github-actions/setup-gcloud@v2
	with:
	version: '>= 363.0.0'

	- name: Check gcloud CLI
	run: gcloud info

	- name: Restore results cache
	uses: actions/cache/restore@v3
	with:
	path: build/malariagen_data_cache
	# Change this key if you ever want to force clear the cache.
	key: results_cache_20230512

	- name: Install conda environment
	uses: mamba-org/setup-micromamba@v2
	with:
	environment-file: environment.yml
	environment-name: selection-atlas
	cache-downloads: true

	- name: Run analysis snakemake workflow
	shell: bash -l {0}
	run: \|
	snakemake -c1 --configfile ci/config.yaml --snakefile workflow/analysis.smk --show-failed-logs

	- name: Run site build snakemake workflow
	shell: bash -l {0}
	run: \|
	snakemake -c1 --configfile ci/config.yaml --snakefile workflow/site.smk --show-failed-logs

	- name: Save results cache
	uses: actions/cache/save@v3
	if: always()
	with:
	path: build/malariagen_data_cache
	# Change this key if you ever want to force clear the cache.
	key: results_cache_20230512

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