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Merge branch 'main' into deploy-apps@main #340

Merge branch 'main' into deploy-apps@main

Merge branch 'main' into deploy-apps@main #340

Workflow file for this run

---
name: Deploy Apps 🚀
on:
push:
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
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
jobs:
deploy:
defaults:
run:
shell: bash
name: Publish 🗞
runs-on: ubuntu-latest
container:
image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest
if: >
!contains(github.event.commits[0].message, '[skip deploy]')
strategy:
fail-fast: false
matrix:
directory:
[
"RNA-seq",
"basic-teal",
"efficacy",
"exploratory",
"longitudinal",
"early-dev",
"patient-profile",
"python",
"safety",
]
channel: ["stable", "dev"]
steps:
- name: Checkout repo 🛎
uses: actions/checkout@v3
- name: Set channel related constants
run: |
if [ "${{ matrix.channel }}" = "stable" ]; then
echo "BRANCH_NAME=deploy-apps@main" >> $GITHUB_ENV # TODO: Change the branch name to main
else
echo "BRANCH_NAME=deploy-apps@dev" >> $GITHUB_ENV # TODO: Change the branch name to deval
fi
- name: Check if cypress test exists
id: find-cypress
run: |
if [ -d ${{ 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
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'
working-directory: ${{ matrix.directory }}/js
run: |
npm i
- name: Restore renv from cache
uses: actions/cache@v3
env:
CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ matrix.channel }}
with:
path: ${{ matrix.directory }}/renv/library
key: ${{ env.CACHE_KEY }}-${{ hashFiles(format('{0}/renv.lock', matrix.directory)) }}
restore-keys: ${{ env.CACHE_KEY }}-
- name: Update renv.lock file with updated GitHub packages
shell: Rscript {0}
run: |
setwd("${{ matrix.directory }}")
lockfile <- renv::lockfile_read()
pkg_name_structure <- ifelse("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s")
for (package in lockfile$Packages) {
if (package$Source == "GitHub") {
renv::record(sprintf(pkg_name_structure, package$RemoteUsername, package$Package))
}
}
- name: Install R packages using renv and update the renv snapshot
shell: Rscript {0}
working-directory: ${{ matrix.directory }}
run: |
options(renv.config.cache.symlinks = FALSE)
lockfile_pkgs <- renv::lockfile_read()$Package
github_pkgs <- names(lockfile_pkgs)[sapply(lockfile_pkgs, function(x) x$Source == "GitHub")]
renv::restore(clean = TRUE)
renv::update(exclude = github_pkgs)
renv::snapshot()
- name: Print the new renv.lock file for ${{ matrix.directory }}
working-directory: ${{ 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'
continue-on-error: true
uses: cypress-io/github-action@v6
with:
working-directory: ${{ matrix.directory }}/js
start: npm run run-app
wait-on: "http://localhost:3333"
wait-on-timeout: 500
project: ../tests
- name: Install deploy R package dependencies
shell: Rscript {0}
working-directory: ${{ matrix.directory }}
run: |
install.packages(c("BiocManager", "rsconnect"))
- name: Deploy 🖨 ${{ matrix.directory }} 🎨
shell: Rscript {0}
continue-on-error: true
working-directory: ${{ matrix.directory }}
run: |
rsconnect::setAccountInfo(
name = "${{ env.SHINYAPPSIO_ACCOUNT }}",
token = "${{ secrets.SHINYAPPSIO_TOKEN }}",
secret = "${{ secrets.SHINYAPPSIO_SECRET }}",
server = "shinyapps.io"
)
rsconnect::deployApp(
appFiles = c("app.R", list.files("www", full.names = TRUE)),
appName = rsconnect::generateAppName("${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}"),
appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}",
account = "${{ env.SHINYAPPSIO_ACCOUNT }}",
upload = TRUE,
logLevel = "normal",
lint = FALSE,
forceUpdate = TRUE
)
- name: Commit updated renv.lock file
run: |
git config --global user.email "[email protected]"
git config --global user.name "GitHub Action"
git config --global --add safe.directory /__w/teal.gallery/teal.gallery
git fetch
git stash
git checkout ${{ env.BRANCH_NAME }}
git stash apply
git pull
if [ -n "$(git diff --staged)" ]; then
git add ${{ matrix.directory }}/renv.lock
git commit -m "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app"
git push origin ${{ env.BRANCH_NAME }}
else
echo "renv.lock was not modified. Nothing to commit.";
fi