Add functions to calculate cycle closure #829

	name: CI

	on:
	push:
	branches:
	- "main"
	pull_request:
	branches:
	- "main"
	schedule:
	# Run a cron job once daily
	- cron: "0 0 * * *"

	concurrency:
	group: "${{ github.workflow }}-${{ github.ref }}"
	cancel-in-progress: true

	defaults:
	run:
	shell: bash -l {0}

	jobs:
	test:
	name: "tests"
	runs-on: ${{ matrix.os }}-latest
	strategy:
	fail-fast: false
	matrix:
	os: ['ubuntu', 'macos']
	python-version:
	- "3.9"
	- "3.10"
	- "3.11"

	steps:
	- uses: actions/checkout@v2

	- uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	activate-environment: test
	channel-priority: true
	environment-file: devtools/conda-envs/env.yaml
	use-mamba: true
	miniforge-variant: Mambaforge

	- name: Additional info about the build
	run: \|
	uname -a
	df -h
	ulimit -a

	- name: Environment Information
	run: \|
	conda info --all
	conda list
	mamba --version

	- name: Install package
	run: \|
	python -m pip install -e .

	- name: Run tests
	shell: bash -l {0}
	run: \|
	pytest -v --cov=cinnabar --cov-report=xml --cov-report=term --color=yes cinnabar/tests/

	- name: codecov
	if: ${{ github.repository == 'OpenFreeEnergy/cinnabar' && github.event_name != 'schedule'}}
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: ./coverage.xml
	fail_ci_if_error: true
	verbose: true # optional (default = false)

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