Merge branch 'main' of https://github.com/ngs-docs/2023-snakemake-boo… #28

	name: Run tests

	on:
	push:
	branches: [main]
	pull_request:

	jobs:
	test:
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [ubuntu-latest]
	python: [3.9]

	name: Python on ${{ matrix.python }}

	steps:
	- name: checkout
	uses: actions/checkout@v3

	# per https://github.com/conda-incubator/setup-miniconda#caching-environments
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	activate-environment: anaconda-client-env
	use-mamba: true
	python-version: ${{ matrix.python }}

	- name: Get Date
	id: get-date
	run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
	shell: bash

	- name: Cache Conda env
	uses: actions/cache@v3
	with:
	path: ${{ env.CONDA }}/envs
	key:
	conda-${{ runner.os }}--${{ runner.arch }}--${{
	steps.get-date.outputs.today }}-${{
	hashFiles('environment-caching.yml') }}-${{ env.CACHE_NUMBER
	}}
	env:
	# Increase this value to reset cache if etc/example-environment.yml has not changed
	CACHE_NUMBER: 0
	id: cache

	- name: Update environment
	run:
	mamba env update -n anaconda-client-env -f environment.yml
	if: steps.cache.outputs.cache-hit != 'true'

	- name: Show Python version
	shell: bash -el {0}
	run: python -V

	- name: Conda info
	shell: bash -el {0}
	run: conda info

	- name: Conda list
	shell: bash -el {0}
	run: conda list

	- name: Cache cargo env
	uses: Swatinem/rust-cache@v2

	- name: Install mdbook
	shell: bash -el {0}
	run: cargo install mdbook mdbook-admonish mdbook-cmdrun

	- name: Run tests
	shell: bash -el {0}
	run: make test

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