Merge pull request #221 from phac-nml/development #422

	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 d1e607b8989260c7b6a3fbce8fa3204ecfc09022 --pointfinder-commit 694919f59a38980204009e7ade76bf319cb7df0b --plasmidfinder-commit c18e08c17a5988d4f075fc1171636e47546a323d'

	strategy:
	fail-fast: False
	matrix:
	include:
	- python-version: "3.9"
	other-packages: "mlst numpy pandas"

	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 -n base conda-libmamba-solver
	conda config --set solver libmamba
	conda install Cython blast git perl-list-moreutils ${{ 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: \|
	pip install pytest
	pytest

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