Merge in short motif code #711

	name: Python application

	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
	# - uses: actions/cache@v2
	# with:
	# path: ~/.cache/pip
	# key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	# restore-keys: \|
	# ${{ runner.os }}-pip-
	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest numpy==1.18.5
	pip install -r requirements.txt -r requirements_TCRdist.txt -r requirements_DeepRC.txt
	- name: Install CompAIRR
	run: \|
	git clone https://github.com/uio-bmi/compairr.git
	make -C compairr
	# - 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: Test with pytest
	env:
	PYTHONFAULTHANDLER: 1
	run: python -m pytest

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