Fix dependencies #184

	name: CI

	on: [push, pull_request]

	jobs:
	build-linux:
	runs-on: ubuntu-20.04
	strategy:
	max-parallel: 5
	matrix:
	python-version: [3.6, 3.7, 3.8, 3.9]

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	conda config --add channels bioconda
	conda config --add channels conda-forge
	# conda env update --file environment.yml --name base
	python -m pip install --upgrade pip
	pip install -r requirements.txt
	pip install -e .
	- name: Lint with flake8
	run: \|
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,E501,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
	run: \|
	conda install pytest
	pytest

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