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### Changes made
1. Removes `renv` from all the nine apps
2. Adds front-end tests for these seven apps (all except `early-dev` and
`python`):
`RNA-seq`, `basic-teal`, `efficacy`, `exploratory`, `longitudinal`,
`patient-profile`, `safety`
3. Updates the `deploy.yaml` workflow:
1. Runs the cypress tests when they are present in the app directory
2. Deploy two versions of apps to RSConnect. `NEST_<APPNAME>_main` and
`NEST_<APPNAME>_release`. The `_main` suffix apps install the teal
packages from https://insightsengineering.r-universe.dev while the
`_release` suffix apps install the teal packages from
https://pharmaverse.r-universe.dev
4. Updates to the `_internal/utils/sourceme.R` to install the packages
from r-universe instead of `renv.lock`.
5. Changes to the appropriate readme files.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -3,20 +3,18 @@ name: Deploy Apps 🚀 | |
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| tags: | ||
| - "*" | ||
| workflow_dispatch: | ||
| #schedule: | ||
| # - cron: '12 3 * * *' | ||
| 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: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| jobs: | ||
| deploy: | ||
|
|
@@ -29,45 +27,143 @@ jobs: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | ||
| if: > | ||
| !contains(github.event.commits[0].message, '[skip deploy]') | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| directory: | ||
| [ | ||
| "RNA-seq", | ||
| "basic-teal", | ||
| "efficacy", | ||
| "exploratory", | ||
| "longitudinal", | ||
| "early-dev", | ||
| "patient-profile", | ||
| "python", | ||
| "safety", | ||
| ] | ||
| channel: ["stable", "dev"] | ||
| steps: | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Set channel related constants | ||
| run: | | ||
| if [ "${{ matrix.channel }}" = "stable" ]; then | ||
| echo "BRANCH_NAME=main" >> $GITHUB_ENV # TODO: Change the branch name to main | ||
| else | ||
| echo "BRANCH_NAME=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: | ||
| path: ${{ github.event.repository.name }} | ||
| node-version: 16 | ||
|
|
||
| - name: Overwrite the global Rprofile ✍️ | ||
| - name: Restore renv from cache | ||
| uses: actions/cache@v3 | ||
| env: | ||
| CACHE_KEY: renv-${{ 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: ${{ env.CACHE_KEY }}- | ||
|
|
||
| - name: Update renv.lock file with updated GitHub packages | ||
| shell: Rscript {0} | ||
| run: | | ||
| cat > /usr/local/lib/R/etc/Rprofile.site <<RPROFILE | ||
| options( | ||
| repos = c( | ||
| Pharmaverse = "https://pharmaverse.r-universe.dev", | ||
| CRAN = "https://cloud.r-project.org", | ||
| BioC = BiocManager::repositories() | ||
| ), | ||
| download.file.method = 'libcurl', | ||
| HTTPUserAgent = sprintf( | ||
| "R/%s R (%s)", | ||
| getRversion(), | ||
| paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"]) | ||
| ) | ||
| ) | ||
| RPROFILE | ||
| setwd("${{ 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: Deploy apps 🖨 ${{ github.event.repository.name }} 🎨 | ||
| - name: Install R packages using renv and update the renv snapshot | ||
| shell: Rscript {0} | ||
| working-directory: ${{ matrix.directory }} | ||
| run: | | ||
| Sys.setenv(GITHUB_PAT="${{ secrets.GITHUB_TOKEN }}") | ||
| devtools::install_local( | ||
| ".", | ||
| upgrade = "never", | ||
| dependencies = TRUE | ||
| 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: | ||
| build: npm install cypress --save-dev | ||
| working-directory: ${{ matrix.directory }}/tests | ||
| start: npm run run-app | ||
| wait-on: "http://localhost:3333" | ||
| wait-on-timeout: 500 | ||
|
|
||
| - 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} | ||
| working-directory: ${{ matrix.directory }} | ||
| run: | | ||
| rsconnect::setAccountInfo( | ||
| name = "${{ env.SHINYAPPSIO_ACCOUNT }}", | ||
| token = "${{ secrets.SHINYAPPSIO_TOKEN }}", | ||
| secret = "${{ secrets.SHINYAPPSIO_SECRET }}", | ||
| server = "shinyapps.io" | ||
| ) | ||
| teal.gallery::deploy_all_apps( | ||
| api_key = "${{ secrets.SHINYAPPSIO_TOKEN }}", | ||
| api_secret = "${{ secrets.SHINYAPPSIO_SECRET }}", | ||
| title_prefix = "NEST", | ||
| title_suffix = "${{ github.ref_name }}", | ||
| server = "https://${{ env.SHINYAPPSIO_ACCOUNT }}.shinyapps.io", | ||
| create_manifest = TRUE | ||
| rsconnect::deployApp( | ||
| appFiles = c("app.R"), | ||
| 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 | ||
| ) | ||
| working-directory: ${{ github.event.repository.name }} | ||
| shell: Rscript {0} | ||
| - 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 | ||
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