Test

Speed up index_chains #133

	name: Test

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]
	schedule:
	- cron: "0 5 1,15 * *"

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	test:
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -e {0} # -e to fail on error

	strategy:
	fail-fast: false
	matrix:
	include:
	- os: ubuntu-latest
	python: "3.9"
	- os: ubuntu-latest
	python: "3.10"
	- os: ubuntu-latest
	python: "3.10"
	pip-flags: "--pre"

	env:
	OS: ${{ matrix.os }}
	PYTHON: ${{ matrix.python }}

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python }}
	cache: "pip"
	cache-dependency-path: "**/pyproject.toml"

	- name: Install test dependencies
	run: \|
	python -m pip install --upgrade pip wheel
	- name: Install dependencies
	run: \|
	# Workaround issue with scikit-bio
	# This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
	pip install git+https://github.com/grst/scikit-bio.git@main
	pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion]"
	- name: Test
	env:
	MPLBACKEND: agg
	PLATFORM: ${{ matrix.os }}
	DISPLAY: :42
	run: \|
	pytest -v --cov --color=yes
	- name: Upload coverage
	uses: codecov/codecov-action@v3

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