publish.yml

name: SDS

on:
  workflow_dispatch:
  push:
    branches: main
  pull_request:
    branches: main
  schedule:
    - cron: "0 4 * * *"

env:
  registry: my_registry_name
  DB_HOST: localhost
  DB_USERNAME: postgres

jobs:
  build-deploy:
    runs-on: ubuntu-latest
    permissions:
      contents: write
    services:
      postgres:
        image: postgis/postgis
        env:
          POSTGRES_HOST_AUTH_METHOD: trust
          POSTGRES_DB: postgis
          ALLOW_IP_RANGE: '*'
        ports:
        - 5432:5432
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2

      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.4.2'
          use-public-rspm: true
      - run: /usr/bin/sudo apt install libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev libpq-dev
      - run: R -q -e 'install.packages(c("dbscan", "downlit", "cubelyr", "gstat", "hglm", "igraph", "lme4", "lmtest", "maps", "mapview", "matrixStats", "mgcv", "R2BayesX", "remotes", "rnaturalearth", "rnaturalearthdata", "RPostgres", "sf", "spatstat", "spatialreg", "spdep", "spData", "stars", "tidyverse", "viridis", "xml2", "BH"))'
      - run: wget https://cran.r-project.org/src/contrib/Archive/rgeoda/rgeoda_0.0.10-4.tar.gz
      - run: R CMD INSTALL rgeoda*gz
      - run: R -q -e 'options(timeout = 600); install.packages("tmap",  repos = c("https://r-tmap.r-universe.dev", "https://cloud.r-project.org"))'
      - run: R -q -e 'options(timeout = 600); install.packages("spDataLarge", repos = "https://nowosad.github.io/drat/", type = "source")'
      - run: R -q -e 'options(timeout = 3600); install.packages("starsdata", repos = "https://cran.uni-muenster.de/pebesma", type = "source")'
      - run: R -q -e 'options(timeout = 3600); install.packages("INLA", repos = c(getOption("repos"), INLA = "https://inla.r-inla-download.org/R/stable"))'
      - run: wget -q https://uni-muenster.sciebo.de/s/8mEbeHPOX9GdAYn/download -O sds.zip
      - run: unzip -q sds.zip
      - run: cp -rp sds/aq .
      - run: rm -fr sds      

      - name: Render and Publish
        if: github.event_name != 'pull_request'
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}