test #343

	name: CI Pipeline

	on:
	pull_request:
	branches:
	- main
	- release
	- change-workflow-name

	jobs:
	build:

	runs-on: self-hosted
	timeout-minutes: 60
	steps:
	- name: Checkout repository
	uses: actions/checkout@v2

	- name: setup python
	uses: actions/setup-python@v5
	with:
	python-version: 3.11.8

	- name: Install dependencies
	run: \|
	pip install -r requirements-dev.txt
	pip install .

	# First download before tests as they make use of the downloaded files
	- name: Download all files
	run: \|
	python ci/download_all.py

	- name: Execute unittests
	run: \|
	pytest --cov-report=html:html_cov --cov-branch --cov-report term --cov=helical ci/

	- name: Upload coverage report
	uses: actions/upload-artifact@v4
	with:
	name: coverage-report
	path: html_cov/

	# Does not seem to work but would be nice to have
	# - name: Pytest coverage comment
	# uses: MishaKav/pytest-coverage-comment@main
	# with:
	# pytest-coverage-path: ./pytest-coverage.txt
	# junitxml-path: ./pytest.xml

	- name: Execute Geneformer v1
	run: \|
	python examples/run_models/run_geneformer.py ++model_name="gf-12L-30M-i2048"

	- name: Execute Geneformer v2
	run: \|
	python examples/run_models/run_geneformer.py ++model_name="gf-12L-95M-i4096"

	- name: Execute scGPT
	run: \|
	python examples/run_models/run_scgpt.py

	- name: Execute UCE
	run: \|
	python examples/run_models/run_uce.py

	- name: Execute Hyena
	run: \|
	python examples/run_models/run_hyena_dna.py

	- name: Execute benchmarking
	run: \|
	pip install scanorama
	python examples/run_benchmark.py

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