build

Misc cleanups and improvements (e.g. new adapter mode) #15

	name: build

	on:
	push:
	branches: [ master ]
	pull_request:
	branches: [ master ]

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8
	- name: miniconda handler
	uses: goanpeca/setup-miniconda@v1
	with:
	auto-update-conda: true
	python-version: 3.8
	auto-activate-base: true
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 nose

	- name: Install conda dependencies
	shell: bash -l {0}
	run: \|
	conda install -c bioconda trimmomatic
	conda install -c bioconda flash
	- name: Lint with flake8
	run: \|
	# 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
	- name: Setup install
	run: \|
	python setup.py install
	- name: nosetests
	shell: bash -l {0}
	run: \|
	cd tests
	nosetests -v

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