Deploy Apps 🚀 #254
Workflow file for this run
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--- | |
name: Deploy Apps 🚀 | |
on: | |
push: | |
branches: | |
- main | |
- dev | |
tags: | |
- "*" | |
workflow_dispatch: | |
schedule: | |
- cron: "12 3 * * *" | |
concurrency: | |
group: publish-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
env: | |
SHINYAPPSIO_ACCOUNT: genentech | |
APP_PREFIX: NEST | |
jobs: | |
deploy: | |
defaults: | |
run: | |
shell: bash | |
name: Publish 🗞 | |
runs-on: ubuntu-latest | |
container: | |
image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
if: > | |
!contains(github.event.commits[0].message, '[skip deploy]') | |
strategy: | |
fail-fast: false | |
matrix: | |
directory: ["basic-teal"] | |
repository: | |
[ | |
"https://insightsengineering.r-universe.dev", | |
"https://pharmaverse.r-universe.dev", | |
] | |
steps: | |
- name: Set CHANNEL | |
run: | | |
if [ "${{ matrix.repository }}" = "https://insightsengineering.r-universe.dev" ]; then | |
echo "CHANNEL=stable" >> $GITHUB_ENV | |
else | |
echo "CHANNEL=release" >> $GITHUB_ENV | |
fi | |
- name: Checkout repo 🛎 | |
uses: actions/checkout@v3 | |
with: | |
path: ${{ github.event.repository.name }} | |
- name: Overwrite the global Rprofile ✍️ | |
run: | | |
cat > /usr/local/lib/R/etc/Rprofile.site <<RPROFILE | |
options( | |
repos = c( | |
Pharmaverse = "${{ matrix.repository }}", | |
CRAN = "https://cloud.r-project.org", | |
BioC = BiocManager::repositories() | |
), | |
download.file.method = 'libcurl', | |
HTTPUserAgent = sprintf( | |
"R/%s R (%s)", | |
getRversion(), | |
paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"]) | |
) | |
) | |
RPROFILE | |
- name: Install jq | |
run: sudo apt-get update && sudo apt-get install -y jq | |
- name: Extract R version from lockfile | |
run: printf 'R_VERSION=%s\n' "$(jq --raw-output .R.Version ${{ github.event.repository.name }}/${{ matrix.directory }}/renv.lock)" >> $GITHUB_ENV | |
- name: Check if cypress test exists | |
id: find-cypress | |
run: | | |
if [ -d ${{ github.event.repository.name }}/${{ matrix.directory }}/tests/cypress ]; then | |
echo "has-cypress-tests=true" >> $GITHUB_OUTPUT | |
else | |
echo "Skipping frontend tests because cypress directory does not exist." | |
echo "has-cypress-tests=false" >> $GITHUB_OUTPUT | |
fi | |
- name: Setup system dependencies for cypress and python app | |
if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
run: > | |
apt-get update && apt-get install --yes | |
libgtk2.0-0 libgbm-dev libnotify-dev libgconf-2-4 xvfb python3.10-venv | |
- name: Setup Node | |
uses: actions/setup-node@v3 | |
if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
with: | |
node-version: 16 | |
- name: Setup npm packages | |
if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
shell: bash | |
working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }}/js | |
run: | | |
npm i | |
- name: Install R packages using renv and update the renv snapshot | |
shell: Rscript {0} | |
working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
run: | | |
options(renv.config.cache.symlinks = FALSE) | |
renv::update() | |
renv::restore(clean = TRUE) | |
renv::snapshot(update = TRUE) | |
- name: Print the new renv.lock file for ${{ matrix.directory }} | |
working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
run: cat renv.lock | |
- name: Front end test to check if the app works fine | |
if: steps.find-cypress.outputs.has-cypress-tests == 'true' | |
uses: cypress-io/github-action@v2 | |
with: | |
working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }}/js | |
start: npm run run-app | |
wait-on: "http://localhost:3333" | |
wait-on-timeout: 500 | |
project: ../tests | |
- name: Deploy 🖨 ${{ matrix.directory }} 🎨 | |
shell: Rscript {0} | |
working-directory: ${{ github.event.repository.name }}/${{ matrix.directory }} | |
run: | | |
install.packages('remotes') | |
remotes::install_version("rsconnect", "0.8.29") | |
rsconnect::setAccountInfo( | |
name = "${{ env.SHINYAPPSIO_ACCOUNT }}", | |
token = "${{ secrets.SHINYAPPSIO_TOKEN }}", | |
secret = "${{ secrets.SHINYAPPSIO_SECRET }}", | |
server = "shinyapps.io" | |
) | |
rsconnect::deployApp( | |
appFiles = "app.R", | |
appName = rsconnect::generateAppName("${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.CHANNEL }}"), | |
appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.CHANNEL }}", | |
account = "${{ env.SHINYAPPSIO_ACCOUNT }}", | |
upload = TRUE, | |
logLevel = "normal", | |
lint = FALSE, | |
forceUpdate = TRUE | |
) | |
- name: Commit updated renv.lock file | |
if: ${{ env.CHANNEL == 'stable' }} #TODO: Will change this to release before merging | |
uses: stefanzweifel/git-auto-commit-action@v4 | |
continue-on-error: true | |
with: | |
repository: ${{ github.event.repository.name }} | |
branch: deploy-apps@main # TODO: switch to the release branch before merging. | |
commit_message: "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app" | |
file_pattern: "${{ matrix.directory }}/renv.lock" | |
commit_user_name: insights-engineering-bot |