Test

Scheduled monthly dependency update for June #101

	name: Test

	on:
	- pull_request

	jobs:
	test:
	runs-on: ${{ matrix.platform }}
	strategy:
	fail-fast: false
	matrix:
	platform:
	- ubuntu-latest
	- windows-latest
	- macos-latest
	python-version:
	- "3.10"
	- "3.11"
	- "3.12"
	numpy-version:
	- "<2"
	- ">=2"

	steps:

	- uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Prerequisites (Linux)
	if: matrix.platform == 'ubuntu-latest'
	run: \|
	sudo apt-get -y install tabix

	- name: Install
	run: \|
	python -m pip install --upgrade pip
	python -m pip install "numpy${{ matrix.numpy-version }}"
	python -m pip install -r requirements_dev_base.txt -r requirements_test.txt -r requirements_dev_optional.txt -r requirements_rtfd.txt
	python -m pip install -e .

	- name: Lint
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 allel --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 allel --count --exit-zero --max-line-length=127 --statistics

	- name: Test
	run: \|
	pytest -v allel

	# - name: Test with doctest
	# if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.numpy-version == '>=2'
	# run: \|
	# pytest -v --cov=allel --doctest-modules allel
	# coverage report -m

	# - name: Build docs
	# if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.numpy-version == '>=2'
	# run: \|
	# cd docs && make html

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