Modify source of total reads used in OGU CPM calc to match that for s… #47

	name: Continuous integration unit testing and lint

	on: [push]

	jobs:
	build:
	strategy:
	matrix:
	python-version: ['3.10']
	os: [ubuntu-latest]
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -el {0}

	steps:
	- name: Check out repository
	uses: actions/checkout@v3

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	#activate-environment: pysyndna
	# environment-file: environment.yml

	- name: Install conda environment
	run: \|
	conda env create -n pysyndna -f environment.yml

	- name: Test with pytest
	run: \|
	conda activate pysyndna
	conda install pytest
	which python
	pip install -e . --no-deps
	pytest

	- name: Lint with flake8
	run: \|
	conda activate pysyndna
	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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