tests

Bump jax from 0.4.13 to 0.4.21 in /requirements #848

	name: tests

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]

	jobs:
	canceller:
	runs-on: ubuntu-22.04
	steps:
	- name: cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{ github.token }}

	tests:
	defaults:
	run:
	shell: bash
	timeout-minutes: 20
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-22.04, macos-12]
	python-version: [3.8, "3.10"]
	env:
	OS: ${{ matrix.os }}
	PYTHON: ${{ matrix.python-version }}

	steps:
	- name: checkout
	uses: actions/checkout@v4

	- name: setup python
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: install dependencies
	run: \|
	python -m pip install -r requirements/minimal.txt
	python -m pip install -r requirements/test.txt

	- name: install bcftools
	run: \|
	# The tests call "bgzip" and "bcftools".
	if [ "$RUNNER_OS" == "Linux" ]; then
	# Ubuntu keeps bgzip in the tabix package.
	sudo apt-get update
	sudo apt-get install bcftools tabix
	elif [ "$RUNNER_OS" == "macOS" ]; then
	brew update
	brew install bcftools
	else
	echo "Don't know how to install bcftools on $RUNNER_OS"
	exit 1
	fi

	- name: run pytest
	run: \|
	python -m pytest \
	-n auto \
	-v \
	--cov=dinf \
	--cov-report=term-missing \
	--cov-report=xml \
	tests

	- name: upload coverage report to codecov
	uses: codecov/codecov-action@v4
	with:
	fail_ci_if_error: true
	env_vars: OS,PYTHON
	# Use upload token to avoid upload failures.
	# https://github.com/codecov/codecov-action/issues/837
	token: d515a3c4-c5cd-4d0f-8bb1-0ebca0450c5a

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