Python cellxgene_census package full unit tests #8

	name: Python cellxgene_census package full unit tests

	# Run all Python unit tets, including those that are too expensive to run frequently.

	on:
	workflow_dispatch: # used for debugging or manual validation

	jobs:
	all_unit_tests:
	runs-on: single-cell-1tb-runner
	steps:
	- name: Install OS dependencies
	run: \|
	sudo apt update
	sudo apt install -y build-essential git-all

	- uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- uses: actions/setup-python@v4
	with:
	python-version: 3.11

	- name: debugging
	run: \|
	pwd
	printenv
	ls -la
	ls -la api/python/cellxgene_census/
	git status
	git describe
	git tag

	- name: Install python dependencies (including experimental)
	run: \|
	python -m pip install -U pip setuptools setuptools_scm wheel
	# debugging
	python -m setuptools_scm -c ./api/python/cellxgene_census/pyproject.toml

	pip install --use-pep517 accumulation-tree # Geneformer dependency needs --use-pep517 for Cython
	pip install -r ./api/python/cellxgene_census/scripts/requirements-dev.txt
	pip install './api/python/cellxgene_census/[experimental]'

	- name: Log debugging info
	run: \|
	python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'

	- name: Pytest (--expensive --experimental)
	run: \|
	PYTHONPATH=. pytest -v --durations=0 -rP --experimental --expensive ./api/python/cellxgene_census/tests/ -k test_incremental_read_obs

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