Exit CP2K applications more reliably #990

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

	name: CI

	on: [push, pull_request]

	permissions:
	contents: read

	defaults:
	run:
	shell: bash -el {0} # Lets conda work

	jobs:
	build:

	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest]
	max-parallel: 5
	runs-on: ${{ matrix.os }}
	timeout-minutes: 30

	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: ${{ matrix.os == 'ubuntu-latest' && 'envs/environment-cpu.yml' \|\| 'envs/environment-macos.yml' }}
	activate-environment: test
	auto-activate-base: true
	auto-update-conda: false
	remove-profiles: true
	architecture: x64
	clean-patched-environment-file: true
	run-post: true
	use-mamba: true
	miniforge-version: latest
	- name: Display Environment
	run: conda list
	- name: Install test dependencies
	run: \|
	pip install -e .[test]
	- name: Lint with flake8
	run: \|
	pip install flake8
	flake8 examol tests
	- name: Add quantum chemistry tools (Linux)
	if: ${{ matrix.os == 'ubuntu-latest' }}
	run: \|
	sudo apt-get update
	sudo apt install -y cp2k
	- name: Run example
	run: examol run examples/redoxmers/spec.py:spec
	- name: Test with pytest
	if: ${{ matrix.os == 'ubuntu-latest' }}
	run: pytest --cov=examol --timeout=300 tests
	- name: Coveralls
	if: ${{ matrix.os == 'ubuntu-latest' }}
	run: \|
	pip install coveralls
	coveralls --service=github
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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