Ensure user-provided PDBs are used for clustering #6

	name: test

	# run unit and integration tests for the ProteinCartography package

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

	jobs:
	test:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- uses: actions/checkout@v3

	- name: Setup conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	python-version: "3.9"
	use-mamba: true
	activate-environment: test-env
	auto-activate-base: false
	# note: the docs claim `use-only-tar-bz2` must be set to true
	# in order for package caching to work properly,
	# but this results in many package-not-found errors,
	# so we set it to false and do not use package caching
	use-only-tar-bz2: false

	- name: Cache the conda env
	uses: actions/cache@v2
	id: cache-conda-env
	with:
	path: ${{ env.CONDA }}/envs
	key:
	conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles('envs/cartography_test.yml') }}

	- name: Create the conda env from which to run snakemake
	run: \|
	mamba env update -n test-env -f envs/cartography_test.yml
	if: steps.cache-conda-env.outputs.cache-hit != 'true'

	- name: Cache the conda envs created by snakemake
	uses: actions/cache@v2
	id: cache-snakemake-conda-envs
	with:
	path: .snakemake/conda
	key:
	conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles('envs/*.yml') }}

	- name: Create the snakemake conda envs
	run: \|
	snakemake --configfile demo/config_actin.yml --use-conda --conda-create-envs-only --cores 1
	if: steps.cache-snakemake-conda-envs.outputs.cache-hit != 'true'

	- name: Run the tests
	run: \|
	pytest -vv -s .

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