Combine all model outputs and target data #12

	name: Combine all model outputs and target data

	on:
	schedule:
	#Sunday at 1:00 AM
	- cron: '0 1 * * 0'
	workflow_dispatch:

	jobs:
	run-r-script:
	runs-on: self-hosted #ubuntu-22.04
	env:
	GITHUB_PAT: ${{ secrets.PERSONAL_GITHUB_TOKEN }}

	steps:
	- name: Checkout repository
	uses: actions/checkout@v3
	with:
	fetch-depth: 0

	# - name: Set up R
	# uses: r-lib/actions/setup-r@v2
	# with:
	# use-public-rspm: true

	# - name: Install R packages
	# run: \|
	# Rscript -e "install.packages(c('lubridate', 'dplyr', 'readr', 'tidyr', 'MMWRweek'))"

	- name: Run all_model_output_and_target_data.R script
	run: \|
	Rscript scripts/all_model_output_and_target_data.R

	- name: Add new files
	run: git add auxiliary-data/

	- name: Commit results
	run: \|
	git config --local user.name "$GITHUB_ACTOR"
	git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
	git commit -am 'added auxiliary data' \|\| echo "No changes to commit"

	- name: Push changes with personal token
	env:
	GITHUB_PAT: ${{ secrets.PERSONAL_GITHUB_TOKEN }}
	run: \|
	git push https://${{ secrets.PERSONAL_GITHUB_TOKEN }}@github.com/ai4castinghub/hospitalization-forecast.git HEAD:main \|\| echo "No changes to commit"

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