retrain #1217
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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 "[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' |