Add parquet and sqlite support; add NNLS-based PEP and Q-value calculation #409

	name: tests

	on:
	push:
	branches:
	- main
	- develop
	pull_request:
	branches:
	- main
	- develop

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	continue-on-error: ${{ matrix.experimental }}
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.8', '3.9', '3.10',]
	os: [ubuntu-latest, windows-latest, macos-latest]
	experimental: [false,]

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest pytest-cov wheel
	pip install -e .
	pip install -e ./tests/system_tests/sample_plugin/.
	- 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
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Run unit and system tests
	run: \|
	pytest -v --cov=mokapot tests/
	- name: Upload coverage to codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	fail_ci_if_error: true

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