update #2103
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| name: update | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 6,12 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_B_I.R') | |
| shell: Rscript {0} | |
| - name: Run R script | |
| run: | | |
| source('scripts/0_excess_deaths_global_estimates_autoupdater_B_II.R') | |
| shell: Rscript {0} | |
| - name: Run R script | |
| run: | | |
| source('scripts/4_excess_deaths_global_estimates_export_for_interactive.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 "[email protected]" | |
| 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' |