Merge pull request #229 from slager/dave

R CMD check tweaks. Fix and fully automate tests.
phuse-org · Feb 25, 2024 · 10551c2 · 10551c2
2 parents 538f2d3 + 09fcd98
commit 10551c2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,24 +38,23 @@ Description: Automate the steps necessary to create a validation ready package
     situations to provide documentation for validation.
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 Suggests: 
     covr,
     XML,
     pdftools,
     bookdown,
     here,
     xml2,
-    rvest
+    rvest,
+    fs
 Imports:
     desc,
     devtools,
     R6,
     roxygen2,
     lubridate,
-    fs,
     rlang,
     yaml,
     whoami,
@@ -69,7 +68,8 @@ Imports:
     knitr,
     kableExtra,
     testthat,
-    tidyselect
+    tidyselect,
+    rstudioapi
 VignetteBuilder: knitr
 SystemRequirements:
     lua
diff --git a/man/val_init.Rd b/man/val_init.Rd
diff --git a/man/vt_dynamic_referencer.Rd b/man/vt_dynamic_referencer.Rd
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
@@ -0,0 +1,10 @@
+#' Create vt test package silently and non-interactively
+make_vt_test_package <- function(){
+  withr::with_options(
+    list(
+      usethis.quiet = TRUE
+    ),
+    {
+      vt_create_package(rstudio = FALSE, open = FALSE)
+    })
+}
diff --git a/tests/testthat/test-add_file.R b/tests/testthat/test-add_file.R
@@ -1,8 +1,8 @@
 test_that("validation file path finds files within the validation infrastructure, throws error otherwise", {
   withr::with_tempdir({
 
-    vt_use_validation()
-    vt_use_req("example_req.md",username = "sample")
+    make_vt_test_package()
+    vt_use_req("example_req.md", username = "sample", open = FALSE)
 
     fp <- validation_file_path(
       file = "example_req.md",

diff --git a/tests/testthat/test-change_log_handlers.R b/tests/testthat/test-change_log_handlers.R
@@ -1,10 +1,8 @@
 test_that("create change log from template", {
   withr::with_tempdir({
 
-    captured_output <- capture.output(vt_create_package("myTestPkg", open = FALSE))
-    setwd("myTestPkg")
-
-    vt_use_change_log(date = "2021-01-01")
+    make_vt_test_package()
+    vt_use_change_log(date = "2021-01-01", open = FALSE)
 
     expect_true(file.exists("vignettes/validation/change_log.md"))
     expect_equal(readLines("vignettes/validation/change_log.md")[1],
@@ -13,9 +11,8 @@ test_that("create change log from template", {
   })
 
   withr::with_tempdir({
-    captured_output <- capture.output(vt_create_package("myTestPkg", open = FALSE))
-    setwd("myTestPkg")
-    vt_use_change_log()
+    make_vt_test_package()
+    vt_use_change_log(open = FALSE)
     expect_true(file.exists("vignettes/validation/change_log.md"))
     expect_equal(readLines("vignettes/validation/change_log.md")[1],
                  paste("# 0.0.0.9000",format(Sys.Date(), "%Y-%m-%d")))
@@ -27,10 +24,9 @@ test_that("change log not in a package", {
 
   withr::with_tempdir({
 
-    file.create(".here")
-    vt_use_validation()
+    make_vt_test_package()
 
-    vt_use_change_log(date = "2021-01-01", version = "0.0.0.9000")
+    vt_use_change_log(date = "2021-01-01", version = "0.0.0.9000", open = FALSE)
 
     expect_equal(
       vt_scrape_change_log(),
@@ -43,10 +39,8 @@ test_that("change log not in a package", {
 
   withr::with_tempdir({
 
-    file.create(".here")
-    vt_use_validation()
-
-    vt_use_change_log()
+    make_vt_test_package()
+    vt_use_change_log(open = FALSE, version = "1.0")
     expect_equal(
       vt_scrape_change_log(),
       data.frame(version = "1.0",
@@ -62,8 +56,7 @@ test_that("Throw informative error when change log does not exist", {
 
   withr::with_tempdir({
 
-    file.create(".here")
-    vt_use_validation()
+    make_vt_test_package()
 
     expect_error(
       vt_scrape_change_log(),

diff --git a/tests/testthat/test-child_files.R b/tests/testthat/test-child_files.R
@@ -1,6 +1,6 @@
 test_that("child files in pkg", {
   withr::with_tempdir({
-    capture_output <- capture.output({vt_create_package(open = FALSE)})
+    make_vt_test_package()
 
     vt_use_req("req1", username = "a user", open = FALSE)
     vt_use_test_case("testcase1", username = "a user", open = FALSE)
@@ -42,7 +42,7 @@ test_that("child files in pkg", {
 
 test_that("child files outside pkg", {
   withr::with_tempdir({
-     vt_use_validation()
+     make_vt_test_package()
      vt_use_test_case("testcase1", username = "a user", open = FALSE)
      vt_use_req("req1", username = "a user", open = FALSE)
      vt_use_test_code("testcode1", username = "another user", open = FALSE)
@@ -63,7 +63,7 @@ test_that("child files outside pkg", {
 
 test_that("incomplete set", {
   withr::with_tempdir({
-    vt_use_validation()
+    make_vt_test_package()
     vt_use_test_case("testcase1", username = "a user", open = FALSE)
     vt_use_test_case("testcase2", username = "a user", open = FALSE)
     vt_use_req("req1", username = "a user", open = FALSE)
@@ -87,7 +87,7 @@ test_that("incomplete set", {
 
 test_that("compatibility between vt_get_child_files and vt_files", {
   withr::with_tempdir({
-    captured_output <- capture.output({vt_create_package(open = FALSE)})
+    make_vt_test_package()
     vt_use_test_case("testcase1", username = "a user", open = FALSE)
     vt_use_test_case("testcase2", username = "a user", open = FALSE)
     vt_use_req("req1", username = "a user", open = FALSE)
@@ -97,11 +97,12 @@ test_that("compatibility between vt_get_child_files and vt_files", {
     setwd(file.path("vignettes", "validation"))
 
     knitr::opts_knit$set("output.dir"= ".")
+
     rmd_asis <- capture.output({vt_file(child_files)})
-    testthat::expect_equal(rmd_asis[9],
-                           "+ Setup: DOCUMENT ANY SETUP THAT NEEDS TO BE DONE FOR TESTING")
+    testthat::expect_in("+ Setup: DOCUMENT ANY SETUP THAT NEEDS TO BE DONE FOR TESTING",
+                        rmd_asis)
 
-    suppressWarnings(testthat::expect_error(vt_file(basename(child_files))))
+    testthat::expect_error(suppressWarnings(vt_file(basename(child_files))))
 
   })
 })
diff --git a/tests/testthat/test-create_item.R b/tests/testthat/test-create_item.R
@@ -68,7 +68,7 @@ test_that("vt_use_ family works nicely with simple item creation", {
   withr::with_tempdir({
 
     # set up validation infrastructure
-    vt_use_validation()
+    make_vt_test_package()
 
     ## create items
     spec_path <- create_item(
@@ -84,13 +84,13 @@ test_that("vt_use_ family works nicely with simple item creation", {
       type = "test_code")
 
     expect_true(
-      file.exists("validation/requirements/new_dir/new_specification")
+      file.exists("vignettes/validation/requirements/new_dir/new_specification")
     )
     expect_true(
-      file.exists("validation/test_cases/new_dir/new_test_case")
+      file.exists("vignettes/validation/test_cases/new_dir/new_test_case")
     )
     expect_true(
-      file.exists("validation/test_code/new_dir/new_test_code")
+      file.exists("vignettes/validation/test_code/new_dir/new_test_code")
     )
   })
 

diff --git a/tests/testthat/test-evaluate_test_code.R b/tests/testthat/test-evaluate_test_code.R
@@ -375,29 +375,24 @@ test_that("vt_kable_test_code_results returns formatted kable object",{
       ),position = "center"), latex_options = "hold_position")
   )
 
-  output_empty <- vt_kable_test_code_results(data.frame(
+  output_empty_df <- data.frame(
     Test = character(),
     Results = character(),
     Pass_Fail = character(),
     stringsAsFactors = FALSE
-  ))
-
-  expect_equal(
-    output_empty,
-    kable_styling(
-    kable_styling(
-        kable(
-          data.frame(
-            Test = character(),
-            Results = character(),
-            Pass_Fail = character(),
-            stringsAsFactors = FALSE
-          ),
-          escape = FALSE,
-          col.names = c("Test", "Results", "Pass/Fail")
-      ),position = "center"), latex_options = "hold_position")
   )
 
+  output_empty <- vt_kable_test_code_results(output_empty_df)
+
+  output_empty_df2 <- output_empty_df
+  names(output_empty_df2) <- c('Test', 'Results', 'Pass/Fail')
+  output_empty2 <- output_empty_df2 %>%
+    kable(format = 'html') %>%
+    kable_styling(position = "center") %>%
+    kable_styling(latex_options = "hold_position")
+
+  expect_equal(output_empty, output_empty2)
+
 
   skip_on_cran()
   withr::with_tempfile(

diff --git a/tests/testthat/test-lua_dynamic_referencing.R b/tests/testthat/test-lua_dynamic_referencing.R
@@ -114,7 +114,7 @@ test_that("lua numbering for html", {
                           pattern = "Later\\sreference\\sto\\s\\((\\d)\\)\\s-\\s(\\d)",
                           replacement = "\\1")))
   expect_equal(c(1, 1, 2, 2, 1, 3, 2),
-               as.numeric(unlist(lapply(strsplit(list_rendered, ": "), FUN = function(x){x[2]}))))
+               as.integer(sub(".*(\\d{1})$", "\\1", list_rendered)))
 
 })