Reorganize GSEA functions #237

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions

	name: Pegasus CI

	on:
	pull_request:
	branches:
	- master

	jobs:
	build:

	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	sudo apt -q update
	sudo apt install -y libfftw3-dev default-jdk git
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest setuptools wheel cython
	python -m pip install zarr
	python -m pip install git+https://github.com/lilab-bcb/pegasusio@master
	python -m pip install -e .[all]
	- name: Lint with flake8
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	- name: Fetch test data
	run: \|
	sudo apt install -y git
	git clone https://github.com/lilab-bcb/pegasus-test-data.git ./tests/data
	- name: Pipeline test
	run: \|
	bash tests/run_pipeline.sh
	pytest tests/test_pipeline.py
	- name: One sample input test
	run: \|
	bash tests/run_one_sample.sh
	- name: iNMF test
	run: \|
	bash tests/run_inmf.sh
	pytest tests/test_inmf.py

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