From 24f2f8ae6c96206abb5682c8fbb4a8eaeeacb5ea Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:45:23 +0200
Subject: [PATCH 1/3] move quarto render into cleanup script

---
 book/_utils/envir_hook.qmd      |  4 ++--
 book/_utils/save_results.qmd    |  6 +++++-
 package/cleanup                 | 20 ++++++++++++++++++++
 package/tests/testthat/helper.R |  2 +-
 package/tests/testthat/setup.R  | 11 ++++++-----
 5 files changed, 34 insertions(+), 9 deletions(-)
 create mode 100755 package/cleanup

diff --git a/book/_utils/envir_hook.qmd b/book/_utils/envir_hook.qmd
index bd162f3776..d3e384ec2b 100644
--- a/book/_utils/envir_hook.qmd
+++ b/book/_utils/envir_hook.qmd
@@ -5,7 +5,7 @@ knitr::knit_hooks$set(test = function(options, envir, before = FALSE) {
   if (isFALSE(options$eval)) {
     return(NULL)
   }
-  if (isFALSE(testthat::is_checking() || testthat::is_testing())) {
+  if (isFALSE(testthat::is_checking() || testthat::is_testing() || as.logical(Sys.getenv("TLG_CATALOG_PKG_BUILD_RENDER", "FALSE")))) {
     return(NULL)
   }
   if (isFALSE(before)) {
@@ -28,7 +28,7 @@ knitr::knit_hooks$set(test = function(options, envir, before = FALSE) {
 
 knitr::opts_template$set(
   include_if_testing = list(
-    eval = isTRUE(testthat::is_checking() || testthat::is_testing()),
+    eval = isTRUE(testthat::is_checking() || testthat::is_testing() || as.logical(Sys.getenv("TLG_CATALOG_PKG_BUILD_RENDER", "FALSE"))),
     cache = FALSE
   ),
   skip_if_testing = list(
diff --git a/book/_utils/save_results.qmd b/book/_utils/save_results.qmd
index 3d28337a8d..80332c68d8 100644
--- a/book/_utils/save_results.qmd
+++ b/book/_utils/save_results.qmd
@@ -2,7 +2,11 @@
 #| renv.ignore: TRUE
 if (exists("tenv")) {
   filename <- paste0(gsub("\\.rmarkdown$", "", knitr::current_input(dir = TRUE)), ".rds")
-  filepath <- gsub(normalizePath(Sys.getenv("QUARTO_PROJECT_DIR")), file.path(Sys.getenv("QUARTO_TESTTHAT_DATA_PATH"), Sys.getenv("QUARTO_PROFILE")), filename)
+  filepath <- gsub(
+    normalizePath(Sys.getenv("QUARTO_PROJECT_DIR")),
+    file.path(Sys.getenv("TLG_CATALOG_PKG_TEST_DATA_PATH"), Sys.getenv("QUARTO_PROFILE")),
+    filename
+  )
   if (!dir.exists(dirname(filepath))) {
     dir.create(dirname(filepath), recursive = TRUE)
   }
diff --git a/package/cleanup b/package/cleanup
new file mode 100755
index 0000000000..19b89b32d2
--- /dev/null
+++ b/package/cleanup
@@ -0,0 +1,20 @@
+#!/bin/sh
+
+# See https://github.com/insightsengineering/tlg-catalog/issues/272
+# This script addresses R CMD CHECK notes caused by the tests/testthat/_book symlink.
+# It renders the book (which saves the output for snapshot testing) and removes the symlink.
+# Executed during the R CMD BUILD "running ‘cleanup’" step, it ensures a smaller package tarball without the symlink and eliminates R CMD CHECK notes.
+
+export TLG_CATALOG_PKG_BUILD_RENDER=TRUE
+export TLG_CATALOG_PKG_TEST_DATA_PATH=$(realpath "./tests/testthat/_data")
+if [ "$TLG_CATALOG_PKG_BUILD_RENDER" = "TRUE" ]; then
+  echo "Rendering Quarto book..."
+  quarto render tests/testthat/_book/ --no-cache
+  echo "Quarto book rendered."
+else
+  echo "Skipping Quarto book rendering."
+fi
+
+rm -rf tests/testthat/_book
+
+exit 0
\ No newline at end of file
diff --git a/package/tests/testthat/helper.R b/package/tests/testthat/helper.R
index 3afbb520be..bfe5f93536 100644
--- a/package/tests/testthat/helper.R
+++ b/package/tests/testthat/helper.R
@@ -1,5 +1,5 @@
 test_article <- function(article_path) {
-  if (isTRUE(if_render_articles)) {
+  if (isTRUE(if_render_articles) && isTRUE(if_book_exists)) {
     quarto::quarto_render(
       file.path(test_book_path, article_path),
       as_job = FALSE,
diff --git a/package/tests/testthat/setup.R b/package/tests/testthat/setup.R
index 1248826f75..89969cc438 100644
--- a/package/tests/testthat/setup.R
+++ b/package/tests/testthat/setup.R
@@ -1,7 +1,7 @@
 test_profile <- Sys.getenv("QUARTO_PROFILE", "stable")
 test_book_path <- testthat::test_path("_book")
 test_data_path <- testthat::test_path("_data")
-Sys.setenv("QUARTO_TESTTHAT_DATA_PATH" = normalizePath(test_data_path))
+Sys.setenv("TLG_CATALOG_PKG_TEST_DATA_PATH" = normalizePath(test_data_path))
 
 # Flags for developers
 # use it if you want to disable render of book or render individual articles instead
@@ -10,8 +10,9 @@ Sys.setenv("QUARTO_TESTTHAT_DATA_PATH" = normalizePath(test_data_path))
 # (ii) set if_render_article to TRUE
 # (iii) assure proper value of `test_profile` ("development" or "stable")
 # (iv) run `devtools::test(filter = "<article_name>")`
-if_render_book <- TRUE # Remember to change this to FALSE if you want to render articles (otherwise loop)
-if_render_articles <- !if_render_book
+if_book_exists <- file.exists(test_book_path)
+if_render_book <- FALSE # Remember to change this to FALSE if you want to render articles (otherwise loop)
+if_render_articles <- FALSE
 if_test_plots <- FALSE # Additional option for optional skip of local plot tests
 # Example for render articles (NOTE: KEEP THESE COMMENTED WHEN RUNNING!!):
 # setwd("package")
@@ -26,7 +27,7 @@ if (isTRUE(if_render_book) && isTRUE(if_render_articles)) {
   stop("Render both book and articles at the same time is not efficient! Please set one of them to FALSE.")
 }
 
-if (isTRUE(if_render_book)) {
+if (isTRUE(if_render_book) && isTRUE(if_book_exists)) {
   cat("Start rendering the book...\n")
   quarto::quarto_render(
     test_book_path,
@@ -41,4 +42,4 @@ if (isTRUE(if_render_book)) {
 
 # clean up
 withr::defer(Sys.unsetenv("QUARTO_PROFILE"), testthat::teardown_env())
-withr::defer(Sys.unsetenv("QUARTO_TESTTHAT_DATA_PATH"), testthat::teardown_env())
+withr::defer(Sys.unsetenv("TLG_CATALOG_PKG_TEST_DATA_PATH"), testthat::teardown_env())

From f3ca63966783fbf5353751dba34f63616db1a5de Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Tue, 15 Oct 2024 17:03:18 +0200
Subject: [PATCH 2/3] fix notes

---
 package/cleanup                          | 3 ++-
 package/tests/testthat/_data/.gitignore  | 2 +-
 package/tests/testthat/_data/.rbuildkeep | 0
 package/tests/testthat/_data/README.md   | 3 +++
 4 files changed, 6 insertions(+), 2 deletions(-)
 delete mode 100644 package/tests/testthat/_data/.rbuildkeep
 create mode 100644 package/tests/testthat/_data/README.md

diff --git a/package/cleanup b/package/cleanup
index 19b89b32d2..1a51c8d3d8 100755
--- a/package/cleanup
+++ b/package/cleanup
@@ -6,7 +6,8 @@
 # Executed during the R CMD BUILD "running ‘cleanup’" step, it ensures a smaller package tarball without the symlink and eliminates R CMD CHECK notes.
 
 export TLG_CATALOG_PKG_BUILD_RENDER=TRUE
-export TLG_CATALOG_PKG_TEST_DATA_PATH=$(realpath "./tests/testthat/_data")
+TLG_CATALOG_PKG_TEST_DATA_PATH=$(realpath "./tests/testthat/_data")
+export TLG_CATALOG_PKG_TEST_DATA_PATH
 if [ "$TLG_CATALOG_PKG_BUILD_RENDER" = "TRUE" ]; then
   echo "Rendering Quarto book..."
   quarto render tests/testthat/_book/ --no-cache
diff --git a/package/tests/testthat/_data/.gitignore b/package/tests/testthat/_data/.gitignore
index 63f2535de6..e5af87e9b5 100644
--- a/package/tests/testthat/_data/.gitignore
+++ b/package/tests/testthat/_data/.gitignore
@@ -1,3 +1,3 @@
 *
 !.gitignore
-!.rbuildkeep
\ No newline at end of file
+!README.md
\ No newline at end of file
diff --git a/package/tests/testthat/_data/.rbuildkeep b/package/tests/testthat/_data/.rbuildkeep
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/package/tests/testthat/_data/README.md b/package/tests/testthat/_data/README.md
new file mode 100644
index 0000000000..094be37c3f
--- /dev/null
+++ b/package/tests/testthat/_data/README.md
@@ -0,0 +1,3 @@
+# README
+
+This is an empty file to keep parent dir not empty.

From 582498a9e2438f3509f70340df7642d0fa156d63 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 16 Oct 2024 09:38:40 +0200
Subject: [PATCH 3/3] move flag definition to the workflow

---
 .github/workflows/check.yml | 2 ++
 package/cleanup             | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
index bf47198a4c..f85af9bb73 100644
--- a/.github/workflows/check.yml
+++ b/.github/workflows/check.yml
@@ -32,6 +32,7 @@ jobs:
       additional-env-vars: |
         NOT_CRAN=true
         QUARTO_PROFILE=development
+        TLG_CATALOG_PKG_BUILD_RENDER=TRUE
       concurrency-group: development
   r-cmd-stable:
     if: github.event_name != 'push'
@@ -45,6 +46,7 @@ jobs:
       additional-env-vars: |
         NOT_CRAN=true
         QUARTO_PROFILE=stable
+        TLG_CATALOG_PKG_BUILD_RENDER=TRUE
       concurrency-group: stable
   linter:
     if: github.event_name != 'push'
diff --git a/package/cleanup b/package/cleanup
index 1a51c8d3d8..0c60970014 100755
--- a/package/cleanup
+++ b/package/cleanup
@@ -5,7 +5,6 @@
 # It renders the book (which saves the output for snapshot testing) and removes the symlink.
 # Executed during the R CMD BUILD "running ‘cleanup’" step, it ensures a smaller package tarball without the symlink and eliminates R CMD CHECK notes.
 
-export TLG_CATALOG_PKG_BUILD_RENDER=TRUE
 TLG_CATALOG_PKG_TEST_DATA_PATH=$(realpath "./tests/testthat/_data")
 export TLG_CATALOG_PKG_TEST_DATA_PATH
 if [ "$TLG_CATALOG_PKG_BUILD_RENDER" = "TRUE" ]; then