Update Re estimates #38

	# This workflow is to re-generate wastewater Re estimates

	name: Calculate Wastewater-based Re

	on:
	# Option to manually trigger deploy
	workflow_dispatch:
	push:
	branches:
	- 'master'
	paths:
	# Only run when a relevant file is updated
	- 'data/clean_data_bs.csv'
	- 'data/clean_data_eawag.csv'

	jobs:

	estimate-ww-re:
	runs-on: macOS-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	steps:
	# Load repo and install R, package dependencies
	- uses: actions/checkout@v3
	- uses: r-lib/actions/setup-r@v2
	- uses: r-lib/actions/setup-r-dependencies@v2 # install (possibly cached) dependencies from DESCRIPTION

	# Run R script
	- name: Estimate Re
	run: Rscript R/estimate_wastewater_re.R

	# Commit new files to data folder
	- name: Commit files
	run: \|
	git config --local user.name actions-user
	git config --local user.email "[email protected]"
	git add app/data/ww_loads.csv
	git add app/data/ww_re_estimates.csv
	git commit -am "GH ACTION calculate-ww-re $(date)"
	git fetch; git merge
	git push origin master

Provide feedback