separate testing and coverage #123

	name: Testing and Coverage

	on: [ push ]

	jobs:
	test:
	name: Test
	runs-on: ${{ matrix.os }}-latest
	strategy:
	max-parallel: 6
	fail-fast: false
	matrix:
	os: [ "ubuntu", "macos" ]
	python-version: [ "3.10", "3.11", "3.12" ]
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- name: checkout
	uses: actions/checkout@v3
	- name: Setup env
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	mamba-version: '*'
	use-mamba: true
	channels: conda-forge, defaults, bioconda
	channel-priority: true
	- uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	- name: Install conda dependencies
	run: mamba install -c bioconda -y mafft
	- name: Install self with pip
	run: pip install .
	- name: Install test dependencies
	run: mamba install -c conda-forge -y pytest pytest-cov coveralls
	- name: Run tests
	run: >
	pytest
	--cov=lXtractor
	--cov-branch
	--cov-report=xml # Changed to XML format for interoperability
	- name: Upload coverage data
	uses: actions/upload-artifact@v3
	with:
	name: coverage-report-${{ matrix.python-version }}
	path: coverage-report-${{ matrix.python-version }}.xml

	publish-coverage:
	name: Coverage
	needs: test
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v3
	- name: Download coverage data
	uses: actions/download-artifact@v3
	with:
	name: coverage-report-3.10
	path: coverage-report-3.10.xml
	- name: Publish Coverage
	run: coveralls --service=github
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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