Merge pull request #8 from dpeerlab/fix-watershed #38

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python package

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.8", "3.9", "3.10"]

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	cache-dependency-path: \|
	'requirements.txt'
	'setup.py'
	- name: Install geos for shapely
	run: sudo apt-get install libgeos-dev
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements.txt
	- name: Install package
	run: python -m pip install -e .
	- name: Mock .merlinenv
	run: printf 'DATA_HOME=~\nANALYSIS_HOME=~\nPARAMETERS_HOME=~\n' > ~/.merlinenv
	- name: Test with pytest
	run: \|
	pytest --cov --cov-report=xml
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: coverage.xml

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