Include more unittests #46

	name: CI Pipeline

	on:
	pull_request:
	branches:
	- main

	jobs:
	build:

	runs-on: ubuntu-latest
	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
	cache: 'pip' # caching pip dependencies

	- name: Cache download files
	uses: actions/cache@v3
	with:
	path: /home/runner/.cache/helical
	key: ${{ runner.os }}-downloads-${{ hashFiles('**/ci/download_all.py') }}

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	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: DEBUG
	run: \|
	ls -ltr /home/runner/.cache/helical


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

	# 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 scGPT
	# run: \|
	# python examples/run_scgpt.py
	# - name: Execute Geneformer
	# run: \|
	# python examples/run_geneformer.py
	# - name: Execute UCE
	# run: \|
	# python examples/run_uce.py
	# - name: Execute Hyena
	# run: \|
	# python examples/run_hyena_dna.py

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