Fix initially blank mutations #189

	name: Tests

	on:
	pull_request:
	push:
	branches: [main, test]

	jobs:
	pre-commit:
	name: Lint
	runs-on: ubuntu-latest
	steps:
	- name: Cancel Previous Runs
	uses: styfle/[email protected]
	with:
	access_token: ${{ github.token }}
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	- uses: pre-commit/[email protected]

	test:
	name: Python
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	python: [ "3.11" ]
	os: [ ubuntu-latest, ]
	defaults:
	run:
	shell: bash
	steps:
	- name: Cancel Previous Runs
	uses: styfle/[email protected]
	with:
	access_token: ${{ github.token }}

	- name: Checkout
	uses: actions/checkout@v3

	- uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	cache: 'pip'

	- name: Install deps
	run: pip install -r requirements.txt

	- name: Tests with numba
	run: coverage run --source=tsbrowse -m pytest -x tests

	- name: Tests with coverage (no numba)
	run: TSBROWSE_DISABLE_NUMBA=1 coverage run --source=tsbrowse -m pytest -x tests

	- name: Create Screenshot
	run: \|
	msp simulate --length 1000 --recombination-rate 0.01 --mutation-rate 0.01 100 out.trees
	python -m tsbrowse preprocess out.trees
	python -m tsbrowse screenshot out.tsbrowse mutations
	python -m tsbrowse screenshot out.tsbrowse edges
	python -m tsbrowse screenshot out.tsbrowse nodes


	- name: Upload Screenshot Artifact
	uses: actions/upload-artifact@v3
	with:
	name: screenshots
	path: "*.png"



	- name: Upload coverage
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: \|
	coveralls --service=github

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