Fix aggregate inclusion binding threshold and add new --aggregate-inclusion-count-limit parameter #999

	name: pVACtools tests

	on:
	push:
	branches: [ master, staging, hotfix ]
	pull_request:
	types: [opened, synchronize, edited, reopened]
	branches: [ master, staging, hotfix]

	jobs:
	run_tests:
	name: "Test pVACtools in various Python versions"

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']

	steps:
	- name: Maximize build space
	uses: AdityaGarg8/remove-unwanted-software@v2
	with:
	remove-android: 'true'
	remove-dotnet: 'true'
	remove-haskell: 'true'
	remove-codeql: 'true'
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install system dependencies
	run: \|
	sudo apt-get -qq update
	sudo apt-get install -y ghostscript
	sudo apt-get install -y gcc
	sudo apt-get install -y pandoc
	pip install pypandoc==1.7.2
	pip install coverage
	pip install coveralls
	- name: Install Python dependencies
	run: \|
	pip install polars==0.16.18
	pip install pypandoc==1.7.2
	pip install "tensorflow<2.16"
	pip install git+https://github.com/griffithlab/bigmhc.git#egg=bigmhc
	pip install git+https://github.com/griffithlab/deepimmuno.git#egg=deepimmuno
	pip install -e .
	mhcflurry-downloads fetch
	- name: List installed packages
	run: \|
	pip list
	- name: Run tests
	env:
	TEST_FLAG: 1
	run: coverage run --source=pvactools.lib,pvactools.tools -m unittest discover -v -s tests
	- name: Coveralls
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: coveralls --service=github

Provide feedback