Merge pull request #109 from OxfordIHTM/dev #60

	# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
	# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
	on:
	push:
	branches: [main, master]
	pull_request:
	branches: [main, master]
	release:
	types: [published]
	workflow_dispatch:

	name: report

	jobs:
	report:
	runs-on: ubuntu-latest
	container: rocker/geospatial:4.3.2
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	permissions:
	contents: write
	steps:
	- uses: actions/checkout@v4

	- name: Install system dependencies
	run: \|
	apt-get update && apt-get install -y --no-install-recommends \
	libxt6 libglpk-dev rsync

	- name: Install R packages
	run: \|
	install.packages(
	c("rmarkdown", "openxlsx", "stringr", "remotes", "here",
	"lme4", "forcats", "plotly", "patchwork", "kableExtra")
	)
	shell: Rscript {0}

	- name: Build reports
	run: \|
	rmarkdown::render(
	"reports/case_study.Rmd",
	output_dir = "docs",
	knit_root_dir = here::here()
	)
	rmarkdown::render(
	"reports/sudan_health_nutrition.Rmd",
	output_file = "index.html",
	output_dir = "docs",
	knit_root_dir = here::here()
	)
	shell: Rscript {0}

	- name: Deploy to GitHub pages 🚀
	if: github.event_name != 'pull_request'
	uses: JamesIves/[email protected]
	with:
	clean: false
	branch: gh-pages
	folder: docs

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