Merge pull request #32 from Clinical-Genomics/update-zipp #44

	name: Python Master Workflow
	on:
	push:
	branches:
	- 'master'

	jobs:
	codecov:
	name: Codecov Workflow
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.10"]

	steps:

	- name: Git checkout
	uses: actions/[email protected]

	- name: Get Conda
	uses: conda-incubator/[email protected]
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}

	# Need to add shell to make conda environments work
	- name: Install spring
	shell: bash -l {0}
	run: \|
	conda install -c bioconda spring

	- name: Install samtools
	shell: bash -l {0}
	run: \|
	conda install -c bioconda samtools

	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	python -m pip install --upgrade pip
	python setup.py install

	- name: Generate coverage report
	shell: bash -l {0}
	run: \|
	pip install pytest
	pip install pytest-cov
	pip install pytest-mock
	pytest --cov=./ --cov-report xml --cov-report term

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v1
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests

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