added citation, updated sample sheet handling #2

	name: Continuous integration unit testing and lint

	on: [push]

	jobs:
	build:
	strategy:
	matrix:
	python-version: ['3.8', '3.10']
	os: [ubuntu-latest]
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- name: Checkout
	uses: actions/checkout@v3

	- name: Get latest QIIME 2 Environment
	shell: bash
	run: \|
	wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml

	- uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: qiime2
	environment-file: qiime2-latest-py38-linux-conda.yml
	auto-activate-base: false

	- name: Install and run unit tests
	run: \|
	conda install pytest
	which python
	pip install -e . --no-deps
	pytest

	- name: Lint with flake8
	run: \|
	conda activate qiime2
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

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