Fix GitHub Actions CI #291

	name: Integration Tests

	on:
	pull_request: # Run on all pull requests
	push:
	branches: # Run on any push to master and development
	- master
	- development
	schedule: # Run weekly on master and development
	- cron: 0 2 * * 0
	branches: master
	- cron: 0 2 * * 0
	branches: development


	jobs:
	build:
	runs-on: ubuntu-latest

	env:
	DATABASE_COMMITS: '--resfinder-commit fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd --pointfinder-commit 8c694b9f336153e6d618b897b3b4930961521eb8 --plasmidfinder-commit 1a443a19a1142aa1018ef62f0bdbfd871b79eab6'

	strategy:
	fail-fast: False
	matrix:
	include:
	- python-version: "3.7"
	other-packages: "mlst 'numpy <1.23.5' 'pandas <2'"

	steps:
	- uses: actions/checkout@v2

	- name: Setup Conda with Python ${{ matrix.python-version }}
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	activate-environment: staramr-env
	python-version: ${{ matrix.python-version }}

	- name: Install conda packages
	shell: bash -l {0}
	run: \|
	conda info
	conda list
	conda config --add channels defaults
	conda config --add channels conda-forge
	conda config --add channels bioconda
	conda install mamba
	mamba install Cython blast git ${{ matrix.other-packages }} -y

	- name: Setup python packages
	shell: bash -l {0}
	run: \|
	python --version
	python setup.py -q install

	- name: Build database
	shell: bash -l {0}
	run: staramr db build --dir staramr/databases/data ${{ env.DATABASE_COMMITS }}

	- name: Run Tests
	shell: bash -l {0}
	run: python setup.py test

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