Include more unittests #40

	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@v2
	with:
	python-version: 3.11 #install the python needed
	- 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: Execute unittests
	run: \|
	pytest --junitxml=pytest.xml --cov-branch --cov=helical ci/ \| tee pytest-coverage.txt
	- 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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