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publish.yml
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on:
workflow_dispatch:
push:
branches: main
schedule:
## Run once every 10 minutes
- cron: '*/10 * * * *'
name: Quarto Publish
jobs:
build-deploy:
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- name: Check out repository
uses: actions/checkout@v4
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y libcurl4-openssl-dev
- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
- name: Set up R
uses: r-lib/actions/setup-r@v2
- name: Cache R packages
uses: actions/cache@v4
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-r-packages
- name: Install R dependencies
run: |
pkgs <- c("ciw", "dplyr", "DT", "ggplot2", "patchwork", "tidyr", "knitr", "lubridate", "forcats", "remotes")
pkgs <- unique(pkgs)
pkgs <- pkgs[!sapply(pkgs, FUN = requireNamespace)]
install.packages(pkgs)
install.packages("cransays", repos = c("https://bisaloo.r-universe.dev", getOption("repos")))
shell: Rscript {0}
- name: Session information
run: |
quarto --version
Rscript --version
- name: Render
uses: quarto-dev/quarto-actions/render@v2
- name: Did output HTML files change?
id: changed
run: |
git fetch origin gh-pages:gh-pages --depth=1
git checkout -f gh-pages
publish=false
for file in $(cd _site/; find . -name "*.html"); do
echo "${file}:"
diff -u -w "${file}" "_site/${file}" || publish=true
done
git checkout -f main
echo "publish=${publish}"
echo "publish=${publish}" >> "${GITHUB_OUTPUT}"
- name: Publish
if: ${{ steps.changed.outputs.publish == 'true' }}
uses: quarto-dev/quarto-actions/publish@v2
with:
render: "false"
target: gh-pages
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}