bgen

sped up parsing phased genotypes with ploidy=2 and bitdepth=8 #217

	name: bgen

	on:
	push:
	pull_request:
	schedule:
	- cron: "33 3 3 * *"

	jobs:
	build_wheels:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
	python: ["cp37", "cp38", "cp39", "cp310", "cp311"]

	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true

	- name: Build wheels
	uses: pypa/[email protected]
	env:
	CIBW_BUILD: ${{ matrix.python }}-*
	CIBW_SKIP: '*i686'
	CIBW_TEST_COMMAND: "python -m unittest discover -s {project}"

	- uses: actions/upload-artifact@v3
	with:
	path: ./wheelhouse/*.whl

	build_sdist:
	name: Build source distribution
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true

	- uses: actions/setup-python@v4
	name: Install Python
	with:
	python-version: '3.10'

	- name: Build sdist
	run: \|
	python -m pip install --upgrade pip
	pip install cython
	python setup.py sdist
	python setup.py install
	python -m unittest discover

	- uses: actions/upload-artifact@v3
	with:
	path: dist/*.tar.gz

	upload_pypi:
	needs: [build_wheels, build_sdist]
	runs-on: ubuntu-latest
	# upload to PyPI on every tag starting with 'v'
	if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
	# alternatively, to publish when a GitHub Release is created, use the following rule:
	# if: github.event_name == 'release' && github.event.action == 'published'
	steps:
	- uses: actions/download-artifact@v3
	with:
	name: artifact
	path: dist

	- uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.pypi_password }}
	# To test: repository_url: https://test.pypi.org/legacy/

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