Move the colmena thinker inside the module #1669

	name: CI

	on:
	push:
	pull_request:
	schedule:
	- cron: '0 12 * * 1'

	permissions:
	contents: read

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

	jobs:
	build:

	runs-on: ubuntu-latest
	timeout-minutes: 15

	steps:
	- uses: actions/checkout@v3
	- name: Set up environment
	uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: envs/environment-cpu.yml
	- name: Install test dependencies
	run: \|
	pip install -e .[test]
	- name: Add quantum chemistry tools (Linux)
	run: \|
	if [ "$RUNNER_OS" == "Linux" ]; then
	# CP2K package has disappeared as of 21Jan25
	# sudo apt update
	# sudo apt install -y cp2k lammps

	# Link the cp2k.ssmp executable to the cp2k_shell needed for ASE
	mkdir -p bin
	cp2k_path=`which cp2k.ssmp`
	export CP2K_DATA_DIR=`which cp2k.ssmp \| xargs dirname`/../share/cp2k/data/
	echo -e "#!/bin/bash\nCP2K_DATA_DIR=$CP2K_DATA_DIR `which cp2k.ssmp` --shell \$@" > bin/cp2k_shell
	chmod u+x bin/cp2k_shell
	cat `which cp2k_shell`
	echo -n \| ./bin/cp2k_shell --version
	else
	echo "$RUNNER_OS not supported"
	exit 1
	fi
	- name: Lint with flake8
	run: \|
	pip install flake8
	flake8 --exclude mofa/utils mofa tests run_*.py # Ignore utils for now
	- name: Test with pytest
	run: \|
	export PATH=$PATH:`realpath ./bin` # Ensure CP2K is visible
	pytest --cov=mofa --timeout=300 tests
	- name: Coveralls
	run: \|
	pip install coveralls
	coveralls --service=github
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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