Merge dev on main (#147)

Now that the core teal packages are released on CRAN. Our stable deployments should start using them. And, all the breaking changes from `dev` can be safely merged on `main`. Since the module packages are still not released, they will be taken from GitHub until they are released. --------- Signed-off-by: Marcin <[email protected]> Signed-off-by: Vedha Viyash <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: vedhav <[email protected]> Co-authored-by: Marcin <[email protected]> Co-authored-by: edelarua <[email protected]> Co-authored-by: André Veríssimo <[email protected]> Co-authored-by: Vedha Viyash <[email protected]>
insightsengineering · Feb 21, 2024 · 096ae11 · 096ae11
1 parent 58bbd12
commit 096ae11
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -6,6 +6,7 @@ on:
     branches:
       - main
       - dev
+      - deploy
     paths:
       - RNA-seq/**
       - basic-teal/**
@@ -20,10 +21,6 @@ on:
   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
@@ -120,7 +117,7 @@ jobs:
           node-version: 20
 
       - name: Restore renv from cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ matrix.channel }}
         with:
@@ -134,13 +131,18 @@ jobs:
           setwd("${{ matrix.directory }}")
           lockfile <- renv::lockfile_read()
           pkg_name_structure <- ifelse("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s")
+          unreleased_packages <- c(
+            "osprey", "hermes", "goshawk", "teal.modules.general", "teal.modules.clinical",
+            "teal.osprey", "teal.modules.hermes", "teal.goshawk", "nestcolor"
+          )
           for (package in lockfile$Packages) {
               if (package$Source == "GitHub") {
-                  # TODO: After teal.slice is released we have to remove this change.
-                  # This workaround is because update to {bslib} breaks current release of teal.slice
-                  if (package$Package == "teal.slice" && "${{ matrix.channel }}" == "stable") {
-                    renv::record("insightsengineering/teal.slice@103491c67e26a9a85d636bd105a806904a0111ec")
+                print(package$Package)
+                  if (package$Package %in% unreleased_packages) {
+                    print(paste0("Recording ", package$Package, " from main"))
+                    renv::record(sprintf("%s/%s", package$RemoteUsername, package$Package))
                   } else {
+                    print(paste0("Recording ", package$Package, " from stable"))
                     renv::record(sprintf(pkg_name_structure, package$RemoteUsername, package$Package))
                   }
               }
@@ -200,11 +202,24 @@ jobs:
           )
 
       - name: Commit and push changes 📌
-        uses: stefanzweifel/git-auto-commit-action@v5
-        with:
-          commit_message: "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app"
-          file_pattern: "${{ matrix.directory }}/renv/activate.R ${{ matrix.directory }}/renv.lock"
-          commit_user_name: github-actions
-          commit_user_email: >-
-            41898282+github-actions[bot]@users.noreply.github.com
-        continue-on-error: true
+        run: |
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions"
+          git config --global --add safe.directory /__w/teal.gallery/teal.gallery
+          git fetch
+          git stash
+          git checkout ${{ env.BRANCH_NAME }}
+          git pull
+          if [ -n "$(git stash list)" ]; then
+            git stash apply
+          else
+            echo "No stash entries found."
+          fi
+          git add ${{ matrix.directory }}/renv.lock
+          git add ${{ matrix.directory }}/renv/activate.R
+          if [ -n "$(git diff --staged)" ]; then
+            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
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
diff --git a/.lintr b/.lintr
@@ -1 +1,6 @@
-linters: with_defaults(line_length_linter(120))
+linters: linters_with_defaults(
+  line_length_linter = line_length_linter(120),
+  cyclocomp_linter = NULL,
+  object_usage_linter = NULL,
+  object_name_linter = object_name_linter(c("snake_case", "symbols", "UPPERCASE"))
+  )
diff --git a/RNA-seq/app.R b/RNA-seq/app.R
@@ -1,35 +1,27 @@
 library(teal.modules.hermes)
 library(teal.modules.general)
-library(scda.2022)
-library(nestcolor)
-
 options(shiny.useragg = FALSE)
 
 nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png"
 
-# code>
-mae <- hermes::multi_assay_experiment
-mae_data <- dataset("MAE", mae)
+## Data reproducible code ----
+data <- teal_data()
+data <- within(data, {
+  library(scda.2022)
+  library(nestcolor)
+  ADTTE <- scda::synthetic_cdisc_data("rcd_2022_06_27")$adtte %>%
+    dplyr::mutate(is_event = CNSR == 0)
+  MAE <- hermes::multi_assay_experiment
+})
+datanames(data) <- c("ADTTE", "MAE")
 
-adtte <- scda::synthetic_cdisc_data("rcd_2022_06_27")$adtte %>%
-  dplyr::mutate(is_event = CNSR == 0)
-
-data <- teal_data(
-  dataset(
-    "ADTTE",
-    adtte,
-    code = 'adtte <- scda::synthetic_cdisc_data("rcd_2022_06_27")$adtte %>%
-      dplyr::mutate(is_event = CNSR == 0)'
-  ),
-  dataset("MAE", mae)
-)
 
 app <- init(
   data = data,
   modules = modules(
     tm_front_page(
       label = "App Info",
-      header_text = c("Info about input data source" = "This app uses MultiplAssayExperiment data object randomly generated by `scda`, `scda.2022` & `hermes` R packages"),
+      header_text = c("Info about input data source" = "This app uses MultiplAssayExperiment data object randomly generated by `scda`, `scda.2022` & `hermes` R packages"), # nolint: line_length.
       tables = list(`NEST packages used in this demo app` = data.frame(
         Packages = c("teal.modules.hermes", "teal.modules.general", "scda", "scda.2022", "hermes")
       ))
@@ -69,9 +61,9 @@ app <- init(
       mae_name = "MAE"
     )
   ),
+  title = build_app_title("RNA-Seq Analysis Teal Demo App", nest_logo),
   header = tags$span(
     style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;",
-    tags$head(tags$link(rel = "shortcut icon", href = nest_logo), tags$title("RNA-Seq Analysis Teal Demo App")),
     tags$span(
       style = "font-size: 30px;",
       "Example teal app focusing on analysis of RNA-seq data with teal.modules.hermes"
@@ -100,7 +92,10 @@ app <- init(
 body(app$server)[[length(body(app$server)) + 1]] <- quote(
   observeEvent(input$showAboutModal, {
     showModal(modalDialog(
-      tags$p("This teal app is brought to you by the NEST Team at Roche/Genentech. For more information, please visit:"),
+      tags$p(
+        "This teal app is brought to you by the NEST Team at Roche/Genentech.
+        For more information, please visit:"
+      ),
       tags$ul(
         tags$li(tags$a(
           href = "https://github.com/insightsengineering", "Insights Engineering",