options for strict tests; few enhancements (#279)

- part of insightsengineering/coredev-tasks#478 - please read this for more info about the implementation: insightsengineering/coredev-tasks#478 (comment) - removed `teal.data::` from code as it's redundant inside `teal.data` - removed unnecessary empty first line in examples as this is actually being rendered Please review the changes carefully and let me know if there is something you don't like.
insightsengineering · Mar 18, 2024 · 99dd0fc · 99dd0fc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,14 +40,14 @@ Imports:
 Suggests:
     knitr (>= 1.42),
     rmarkdown (>= 2.19),
-    testthat (>= 3.1.5)
+    testthat (>= 3.1.5),
+    withr (>= 2.0.0)
 VignetteBuilder:
     knitr
 RdMacros:
     lifecycle
-Config/Needs/verdepcheck: mllg/checkmate, r-lib/lifecycle, r-lib/rlang,
-    yihui/knitr, rstudio/rmarkdown, insightsengineering/teal.code,
-    r-lib/testthat
+Config/Needs/verdepcheck: insightsengineering/teal.code, mllg/checkmate, r-lib/lifecycle, r-lib/rlang,
+    yihui/knitr, rstudio/rmarkdown, r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US

diff --git a/R/join_keys-extract.R b/R/join_keys-extract.R
@@ -14,7 +14,6 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Getter for join_keys ---
 #'
 #' jk["ds1", "ds2"]
@@ -131,7 +130,6 @@
 #'
 #' @export
 #' @examples
-#'
 #' # Setting a new primary key ---
 #'
 #' jk["ds4", "ds4"] <- "pk4"
@@ -189,7 +187,6 @@
 #'
 #' @export
 #' @examples
-#'
 #' # Setting via x[[i]] <- value ---
 #'
 #' jk <- join_keys()

diff --git a/R/join_keys-parents.R b/R/join_keys-parents.R
@@ -30,7 +30,6 @@ parents.join_keys <- function(x) {
 #' @describeIn parents Retrieves parents of `join_keys` inside `teal_data` object.
 #' @export
 #' @examples
-#'
 #' # Get parents of join_keys inside teal_data object ---
 #'
 #' td <- teal_data(
@@ -56,7 +55,6 @@ parents.teal_data <- function(x) {
 #' @describeIn parents Assignment of parents of `join_keys` object.
 #' @export
 #' @examples
-#'
 #' # Assignment of parents ---
 #'
 #' jk <- join_keys(
@@ -109,7 +107,6 @@ parents.teal_data <- function(x) {
 #' @describeIn parents Assignment of parents of `join_keys` inside `teal_data` object.
 #' @export
 #' @examples
-#'
 #' # Assignment of parents of join_keys inside teal_data object ---
 #'
 #' parents(td) <- list("ADTTE" = "ADSL") # replace existing
@@ -128,7 +125,6 @@ parents.teal_data <- function(x) {
 #' @export
 #'
 #' @examples
-#'
 #' # Get individual parent ---
 #'
 #' parent(jk, "ds2")

diff --git a/R/join_keys.R b/R/join_keys.R
@@ -111,7 +111,6 @@ join_keys.teal_data <- function(...) {
 #' @order 5
 #' @export
 #' @examples
-#'
 #' # Assigning keys via join_keys(x)[i, j] <- value ----
 #'
 #' obj <- join_keys()
@@ -133,7 +132,6 @@ join_keys.teal_data <- function(...) {
 #' @order 5
 #' @export
 #' @examples
-#'
 #' # Setter for join_keys within teal_data ----
 #'
 #' td <- teal_data()

diff --git a/R/verify.R b/R/verify.R
@@ -43,7 +43,9 @@
 #'           e <- 1"
 #' )
 #' tdata4
-#' try(verify(tdata4)) # fails
+#' \dontrun{
+#' verify(tdata4) # fails
+#' }
 #'
 #' @name verify
 #' @rdname verify

diff --git a/man/join_keys.Rd b/man/join_keys.Rd
diff --git a/man/parents.Rd b/man/parents.Rd
diff --git a/man/verify.Rd b/man/verify.Rd
diff --git a/tests/testthat/setup-options.R b/tests/testthat/setup-options.R
@@ -0,0 +1,20 @@
+# `opts_partial_match_old` is left for exclusions due to partial matching in dependent packages (i.e. not fixable here)
+# it might happen that it is not used right now, but it is left for possible future use
+# use with: `withr::with_options(opts_partial_match_old, { ... })` inside the test
+opts_partial_match_old <- list(
+  warnPartialMatchDollar = getOption("warnPartialMatchDollar"),
+  warnPartialMatchArgs = getOption("warnPartialMatchArgs"),
+  warnPartialMatchAttr = getOption("warnPartialMatchAttr")
+)
+opts_partial_match_new <- list(
+  warnPartialMatchDollar = TRUE,
+  warnPartialMatchArgs = TRUE,
+  warnPartialMatchAttr = TRUE
+)
+
+if (isFALSE(getFromNamespace("on_cran", "testthat")()) && requireNamespace("withr", quietly = TRUE)) {
+  withr::local_options(
+    opts_partial_match_new,
+    .local_envir = testthat::teardown_env()
+  )
+}
diff --git a/tests/testthat/test-get_code.R b/tests/testthat/test-get_code.R
@@ -411,7 +411,7 @@ testthat::test_that("ignores occurrence in a function definition in lapply", {
     "b <- lapply(a, FUN = function(x) { x <- x + 1 })",
     "b <- Filter(function(x) x > 2, b)",
     "x <- 1",
-    "print(x)"
+    "identity(x)"
   )
   tdata <- eval_code(teal_data(), code)
   testthat::expect_identical(

diff --git a/vignettes/join-keys.Rmd b/vignettes/join-keys.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Join Keys"
 author: "NEST CoreDev"
-output: 
+output:
   rmarkdown::html_vignette:
     toc: true
 vignette: >
@@ -88,19 +88,19 @@ jk
 | Output of `print(jk)`              | Output annotation                    |
 | ---------------------------------- |:----------------------------------------:|
 | `## A join_keys object containing foreign keys between 3 datasets:` |  **Title** |
-| `## ds1: [col_1]`                |  **Primary keys**<br />_\<dataset name\>_: [_\<primary_keys\>_]                                          | 
-| `##   <-- ds2: [col_1]`          | **Foreign keys**<br /> _(arrow `<--` denotes `ds1` is the parent of `ds2`)_                    | 
-| `##   <-- ds3: [col_1]`          |                                                                               | 
-| `## ds2: [col_1, col_2]`           |                                                                               | 
-| `##   --> ds1: [col_1]`          | arrow `-->` denotes `ds2` is a child of `ds1`                                                                              | 
+| `## ds1: [col_1]`                |  **Primary keys**<br />_\<dataset name\>_: [_\<primary_keys\>_]                                          |
+| `##   <-- ds2: [col_1]`          | **Foreign keys**<br /> _(arrow `<--` denotes `ds1` is the parent of `ds2`)_                    |
+| `##   <-- ds3: [col_1]`          |                                                                               |
+| `## ds2: [col_1, col_2]`           |                                                                               |
+| `##   --> ds1: [col_1]`          | arrow `-->` denotes `ds2` is a child of `ds1`                                                                              |
 | `##   --* (implicit via parent with): ds3` |  **Implicit relationship between `ds2` & `ds3`**<br />_(given that they share common keys with same parent)_    |
-| `## ds3: [col_1, col_3]`           |                                                                               | 
-| `##   --> ds1: [col_1]`          |                                                                               | 
-| `##   --* (implicit via parent with): ds2` |                                                                               | 
-| `## ds4: [no primary keys]`    |                                                                               | 
-| `##   <-> ds5: [col_5]`          |  **Foreign keys** <br />_(arrow `<->` denotes no parent definition between datasets)_      | 
-| `## ds5: [no primary keys]`    |                                                                               | 
-| `##   <-> ds4: [col_4] `         |                                                                               | 
+| `## ds3: [col_1, col_3]`           |                                                                               |
+| `##   --> ds1: [col_1]`          |                                                                               |
+| `##   --* (implicit via parent with): ds2` |                                                                               |
+| `## ds4: [no primary keys]`    |                                                                               |
+| `##   <-> ds5: [col_5]`          |  **Foreign keys** <br />_(arrow `<->` denotes no parent definition between datasets)_      |
+| `## ds5: [no primary keys]`    |                                                                               |
+| `##   <-> ds4: [col_4] `         |                                                                               |
 
 ## Accessing and Modifying keys