Test

update sourmash and snakemake dependencies #163

	name: Test

	on: [push, pull_request]

	jobs:
	test:
	runs-on: ubuntu-latest

	strategy:
	matrix:
	python: [3.9]

	name: Python ${{ matrix.python }}

	# We want to run on external PRs, but not on our own internal PRs as they'll be run by the push to the branch.
	if: github.event_name == 'push' \|\| github.event.pull_request.head.repo.full_name != github.repository

	steps:
	- uses: actions/checkout@v2

	- name: Set up Python ${{ matrix.python }}
	uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python }}

	- run: pip install -U pip setuptools

	- name: Setup conda
	uses: s-weigand/setup-conda@v1
	with:
	activate-conda: true
	- run: conda env update -n base -f environment.yml

	- name: Install coverage dependencies
	run: pip install pytest-cov pytest-dependency

	- name: Build
	run: python setup.py build_ext --inplace

	- name: Install charcoal
	run: pip install -e .

	- run: pytest tests

	# - run: pytest tests --cov=.

	# - name: Upload coverage to Codecov
	# uses: codecov/codecov-action@v1

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