Merge pull request #600 from tskit-dev/post-release #24

	name: Integration tests

	on:
	pull_request:
	push:
	branches: [main, test]
	merge_group:

	jobs:
	end-to-end:
	name: End to end tests
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v4.2.2
	- uses: astral-sh/setup-uv@v6
	with:
	python-version: "3.11"
	version: "0.8.15"
	- name: Install dependencies
	run: uv sync --locked --group test

	- name: Create basedir
	run: \|
	mkdir -p testrun
	gunzip -k tests/data/alignments.fasta.gz

	- name: Import alignments
	run: uv run sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta

	- name: Import metadata
	run: uv run sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv

	- name: Info dataset
	run: uv run sc2ts info-dataset testrun/dataset.zarr

	- name: Run inference
	run: \|
	# doing ~10 days here as this is taking a while
	uv run sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03

	- name: Validate
	run: uv run sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts

	- name: MatchDB
	run: uv run sc2ts info-matches testrun/test.matches.db

	bare-api:
	name: Bare API tests
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v4.2.2
	- uses: astral-sh/setup-uv@v6
	with:
	python-version: "3.11"
	version: "0.8.15"
	- name: Run tests
	run: \|
	# Minimal deps only; avoid picking up conftest and fixtures
	uv run pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py

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