ci: switch to codecov rather than codacy (#110) #82

	name: CI

	on: [push]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version:
	- '3.8'
	- '3.9'
	- '3.10'
	- '3.11'
	- '3.12'

	steps:
	- name: Install Python via conda.
	uses: s-weigand/setup-conda@v1
	with:
	python-version: ${{ matrix.python-version }}
	conda-channels: defaults,bioconda,conda-forge
	- name: Checkout repository
	uses: actions/checkout@v2
	with:
	lfs: true
	- name: Install mamba.
	run: conda install -y mamba
	- name: Install test dependencies via pip
	run: pip install -r requirements/test_black.txt
	- name: Run tests
	run: pytest
	- name: Create text report
	run: coverage report
	- name: Create XML report for codacy
	run: coverage xml
	- name: Upload Python coverage reports to Codecov
	uses: codecov/codecov-action@v3
	with:
	flags: python
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	- name: Check style with black
	run: make black-check
	- name: Check style with flake8
	run: flake8 .

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