Merge pull request #17 from beardymcjohnface/dev #67

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Codecov

	on:
	push:
	branches: [ "main" ]
	paths:
	- '.github/workflows/codecov.yml'
	- 'tests/**'
	- 'trimnami/**'
	- 'setup.py'
	pull_request:
	branches: [ "main" ]
	paths:
	- '.github/workflows/codecov.yml'
	- 'tests/**'
	- 'trimnami/**'
	- 'setup.py'

	permissions:
	contents: read

	jobs:
	tests:
	name: "Python ${{ matrix.python-version }}"
	runs-on: ${{ matrix.os }}

	defaults:
	run:
	shell: bash -el {0}

	strategy:
	matrix:
	os: [ubuntu-latest]
	python-version: ["3.10"]

	steps:
	- uses: "actions/checkout@v3"
	with:
	fetch-depth: 0

	# Setup env
	- uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	miniforge-version: "latest"
	miniforge-variant: Mambaforge
	use-mamba: true
	mamba-version: "*"
	channels: conda-forge,bioconda,defaults
	channel-priority: strict
	python-version: ${{ matrix.python-version }}
	auto-activate-base: false

	- name: "Test and generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
	run: \|
	python -m pip install --upgrade pip
	python -m pip install pytest coverage
	python -m pip install .
	coverage run -m pytest
	coverage xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: coverage.xml
	fail_ci_if_error: true

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