remove verify-warning from the code (#334)

linking to the discussion

insightsengineering/teal#1342 (comment)

- removed verification-warning message from get_code 
- ~~added is_verified method to possibly handle `@verified == FALSE` by
external process. I'm fine to use `@verified` directly in `teal` - I'm
happy also to remove `is_verified` if suggested in review.~~

NEWS.md

@@ -10,6 +10,10 @@
     - do not allow to set a dataset name that do not exist in `teal_data` environment.
     - `teal_data` no longer set default `datanames()` based on `join_keys` names - it uses only data names.
 
+### Miscellaneous
+
+- `get_code` no longer adds `warning` message about failed verification.
+
 # teal.data 0.6.0
 
 ### Enhancements

R/teal_data-get_code.R

@@ -4,7 +4,6 @@
 #'
 #' Retrieve code stored in `@code`, which (in principle) can be used to recreate all objects found in `@env`.
 #' Use `datanames` to limit the code to one or more of the datasets enumerated in `@datanames`.
-#' If the code has not passed verification (with [`verify()`]), a warning will be prepended.
 #'
 #' @section Extracting dataset-specific code:
 #' When `datanames` is specified, the code returned will be limited  to the lines needed to _create_
@@ -114,10 +113,6 @@ setMethod("get_code", signature = "teal_data", definition = function(object, dep
     object@code
   }
 
-  if (!object@verified) {
-    code <- c("warning('Code was not verified for reproducibility.')", code)
-  }
-
   if (deparse) {
     if (length(code) == 0) {
       code

tests/testthat/test-get_code.R

@@ -1,13 +1,11 @@
-warning_message <- "warning('Code was not verified for reproducibility.')"
-
 testthat::test_that("handles empty @code slot", {
   testthat::expect_identical(
     get_code(teal_data(a = 1, code = character(0)), datanames = "a"),
-    warning_message
+    character(0)
   )
   testthat::expect_identical(
     get_code(teal_data(a = 1, code = ""), datanames = "a"),
-    paste0(warning_message, "\n")
+    ""
   )
 })
 
@@ -20,7 +18,7 @@ testthat::test_that("handles the code without symbols on rhs", {
 
   testthat::expect_identical(
     get_code(teal_data(a = 5, code = code), datanames = "a"),
-    paste(warning_message, "a <- 5", sep = "\n")
+    "a <- 5"
   )
 })
 
@@ -29,7 +27,7 @@ testthat::test_that("handles the code included in curly brackets", {
 
   testthat::expect_identical(
     get_code(teal_data(a = 5, code = code), datanames = "a"),
-    paste(warning_message, "a <- 5", sep = "\n")
+    "a <- 5"
   )
 })
 
@@ -545,11 +543,7 @@ testthat::test_that("detects occurrence of a function definition with a @linksto
   tdata <- teal_data(code = code)
   testthat::expect_identical(
     get_code(tdata, datanames = "x"),
-    paste(
-      warning_message,
-      "foo <- function() {\n    env <- parent.frame()\n    env$x <- 0\n}\nfoo()",
-      sep = "\n"
-    )
+    "foo <- function() {\n    env <- parent.frame()\n    env$x <- 0\n}\nfoo()"
   )
 })
 # $ ---------------------------------------------------------------------------------------------------------------
@@ -608,7 +602,6 @@ testthat::test_that("understands @ usage and do not treat rhs of @ as objects (o
   testthat::expect_identical(
     get_code(tdata, datanames = "x"),
     paste(
-      warning_message,
       'setClass("aclass", slots = c(a = "numeric", x = "numeric", y = "numeric"))',
       'x <- new("aclass", a = 1:3, x = 1:3, y = 1:3)',
       sep = "\n"
@@ -617,7 +610,6 @@ testthat::test_that("understands @ usage and do not treat rhs of @ as objects (o
   testthat::expect_identical(
     get_code(tdata, datanames = "a"),
     paste(
-      warning_message,
       'setClass("aclass", slots = c(a = "numeric", x = "numeric", y = "numeric"))',
       'x <- new("aclass", a = 1:3, x = 1:3, y = 1:3)',
       'a <- new("aclass", a = 1:3, x = 1:3, y = 1:3)',
@@ -646,7 +638,6 @@ testthat::test_that("library() and require() are always returned", {
   testthat::expect_identical(
     get_code(tdata, datanames = "x"),
     paste(
-      warning_message,
       "library(random.cdisc.data)",
       "require(dplyr)",
       "library(MultiAssayExperiment)",
@@ -672,7 +663,6 @@ testthat::test_that("data() call is returned when data name is provided as is",
   testthat::expect_identical(
     get_code(tdata, datanames = "x"),
     paste(
-      warning_message,
       "library(random.cdisc.data)",
       "require(dplyr)",
       "library(MultiAssayExperiment)",
@@ -696,7 +686,6 @@ testthat::test_that("data() call is returned when data name is provided as a cha
   testthat::expect_identical(
     get_code(tdata, datanames = "z"),
     paste(
-      warning_message,
       "library(random.cdisc.data)",
       "require(dplyr)",
       "library(MultiAssayExperiment)",

vignettes/teal-data-reproducibility.Rmd

@@ -45,7 +45,6 @@ data_with_data <- teal_data(i = head(iris), code = "i <- head(iris)")
 data_with_data # is unverified
 data_with_data <- within(data_with_data, i$rand <- sample(nrow(i)))
 data_with_data # remains unverified
-cat(get_code(data_with_data)) # warning is prepended
 ```
 
 ### Verification process
@@ -69,7 +68,7 @@ data_right <- teal_data(
     data <- data.frame(x = 11:20)
     data$id <- seq_len(nrow(data))
   })
-)
+) # is unverified
 (data_right_verified <- verify(data_right)) # returns verified object
 ```