retrain.yaml

name: retrain
on:
  workflow_dispatch:
  schedule:
    - cron: "0 00 * * 1"
jobs:
  build:
    runs-on: ubuntu-20.04
    env:
      S3_FOLDER: covid-19-excess-deaths-global-estimates-tracker
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_VERSION: 4.0.3
      NODE_VERSION: 16
    steps:
      - name: Checkout repo
        uses: actions/checkout@v2

      - name: Set up R
        uses: r-lib/actions/setup-r@12d5b556c504a4be89f0dc9779e0de65bf0cfa44
        with:
          r-version: ${{ env.R_VERSION }}

      - name: Set up Node
        uses: actions/setup-node@v2
        with:
          node-version: ${{ env.NODE_VERSION }}

      - name: Set up Ubuntu packages
         # run: sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
        run: sudo apt-get install libcurl4-openssl-dev libssl-dev libfontconfig1-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
         
      - name: Cache R packages
        id: cache
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}
          key: r-v5-${{ env.R_VERSION }}
          restore-keys: r-v5

      - name: Cache node modules
        uses: actions/cache@v2
        env:
          cache-name: cache-node-modules
        with:
          # npm cache files are stored in `~/.npm` on Linux/macOS
          path: ~/.npm
          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
          restore-keys: |
            ${{ runner.os }}-build-${{ env.cache-name }}-
            ${{ runner.os }}-build-
            ${{ runner.os }}-

      - name: Install packages
        if: steps.cache.outputs.cache-hit != 'true'
        run: |
          install.packages(c(
            "devtools",
            "anytime",
            "countrycode",
            "data.table",
            "tidyverse",
            "readxl",
            "googlesheets4",
            "lubridate",
            "maps",
            "progress",
            "WDI",
            "zoo"
          ))
          devtools::install_github('sondreus/agtboost/R-package')
        shell: Rscript {0}

      - name: Run R script
        run: |
          source('scripts/0_excess_deaths_global_estimates_autoupdater_A.R')
        shell: Rscript {0}

      - name: Run R script
        run: |
          source('scripts/0_excess_deaths_global_estimates_autoupdater_C.R')
        shell: Rscript {0}

      - name: Generate minimaps
        run: | 
          cd scripts/minimaps && npm ci
          npm run build

      - name: Commit files
        run: |
          git config --local user.email "action@github.com"
          git config --local user.name "GitHub Action"
          git commit --allow-empty -m "Data auto-update" -a

      - name: Push changes
        uses: ad-m/github-push-action@8407731efefc0d8f72af254c74276b7a90be36e1
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ github.ref }}

      - name: Upload to S3
        run: |
          aws s3 sync ./output-data/output-for-interactive s3://"$AWS_S3_BUCKET"/"$S3_FOLDER" --acl public-read --cache-control "public,max-age=300,proxy-revalidate"
        env:
          S3_FOLDER: ${{ env.S3_FOLDER }}
          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          AWS_REGION: 'us-east-1'
          
      - name: Create Cloudfront invalidation
        run: |
          aws cloudfront create-invalidation --distribution-id "$AWS_CLOUDFRONT_DISTRIBUTION_ID" --paths "/$S3_FOLDER/*"
        env:
          S3_FOLDER: ${{ env.S3_FOLDER }}
          AWS_CLOUDFRONT_DISTRIBUTION_ID: ${{ secrets.AWS_CLOUDFRONT_DISTRIBUTION_ID }}
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          AWS_REGION: 'us-east-1'