Tests

refactor!: remove pybedtools as a dependency. This slightly changes the interpretation of BED files. From now on, the end position of each region will not be included. #41

	name: Tests

	on: [pull_request, workflow_call]

	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	tests:
	name: Test with py${{ matrix.python-version }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11"]

	steps:
	- uses: actions/checkout@v4
	- name: Set up mamba
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: test
	auto-activate-base: false
	python-version: ${{ matrix.python-version }}
	miniforge-version: latest
	miniforge-variant: Mambaforge
	use-mamba: true
	mamba-version: "*"
	- name: Install test dependencies
	shell: bash -el {0}
	run: \|
	mamba install -c conda-forge -c bioconda bcftools pip pytest pytest-cov
	- name: Upgrade pip and install our package
	shell: bash -el {0}
	run: \|
	python -m pip install --upgrade pip setuptools wheel setuptools-scm
	pip install -e .
	- name: Test with pytest
	shell: bash -el {0}
	run: \|
	python -m pytest --cov=. --cov-report term-missing --cov-fail-under 89 --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
	- name: Test command line
	shell: bash -el {0}
	run: \|
	./test/cmdline_tests.sh
	- name: Upload pytest test results
	uses: actions/upload-artifact@v3
	with:
	name: pytest-results-${{ matrix.python-version }}
	path: junit/test-results-${{ matrix.python-version }}.xml
	# Use always() to always run this step to publish test results when there are test failures
	if: ${{ always() }}

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