tests

Implement diplotype clustering, refactor haplotype clustering, and fi… #15

	name: tests
	on:
	push:
	branches:
	- master
	pull_request:
	branches:
	- master
	jobs:
	tests:
	strategy:
	fail-fast: true
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11"]
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v3

	- name: Install poetry
	run: pipx install poetry==1.7.1

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

	- name: Install dependencies
	run: poetry install

	# Run a subset of tests first which run quickly without accessing
	# any remote data in order to fail fast where possible.
	- name: Run fast unit tests
	run: poetry run pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph

	- name: Restore GCS cache
	uses: actions/cache/restore@v3
	with:
	path: gcs_cache
	key: gcs_cache_tests_20231119

	- name: Run full test suite
	run: poetry run pytest --durations=20 -v tests

	- name: Save GCS cache
	uses: actions/cache/save@v3
	if: always()
	with:
	path: gcs_cache
	key: gcs_cache_tests_20231119

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