Merge pull request #191 from mrc-ide/mrc-5791

Make example runner less clever

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly2
 Title: Orderly Next Generation
-Version: 1.99.47
+Version: 1.99.48
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Robert", "Ashton", role = "aut"),

R/cleanup.R

@@ -7,11 +7,11 @@
 ##' directories; orderly2 has similar semantics here to git where
 ##' directories are never directly tracked.
 ##'
-##' For recent `gert` (not yet on CRAN) we will ask git if files are
-##' ignored; if ignored then they are good candidates for deletion! We
-##' encourage you to keep a per-report `.gitignore` that lists files
-##' that will copy into the source directory, and then we can use that
-##' same information to clean up these files after generation.
+##' For recent `gert` we will ask git if files are ignored; if ignored
+##' then they are good candidates for deletion! We encourage you to
+##' keep a per-report `.gitignore` that lists files that will copy
+##' into the source directory, and then we can use that same
+##' information to clean up these files after generation.
 ##' Importantly, even if a file matches an ignore rule but has been
 ##' committed to your repository, it will no longer match the ignore
 ##' rule.
@@ -65,6 +65,8 @@
 ##'
 ##' # Do the actual deletion:
 ##' orderly2::orderly_cleanup("data", root = path)
+##'
+##' fs::dir_delete(path)
 orderly_cleanup <- function(name = NULL, dry_run = FALSE, root = NULL) {
   status <- orderly_cleanup_status(name, root)
   n <- length(status$delete)

R/example.R

@@ -19,18 +19,20 @@
 ##' @examples
 ##' path <- orderly2::orderly_example("default")
 ##' orderly2::orderly_list_src(root = path)
+##'
+##' fs::dir_delete(path)
 orderly_example <- function(name, ..., dest = NULL) {
   match_value(name, "default", call = environment())
   if (is.null(dest)) {
-    dest <- withr::local_tempfile(.local_envir = parent.frame())
+    dest <- tempfile("orderly2_ex_")
   } else {
-    assert_scalar_character(dest, call = environment())
-  }
-  if (file.exists(dest)) {
-    cli::cli_abort("The path '{dest}' cannot exist")
+    assert_scalar_character(dest)
+    if (file.exists(dest)) {
+      cli::cli_abort("The path '{dest}' must not exist")
+    }
   }
+  orderly_init(..., root = dest)
   src <- orderly2_file("example")
-  fs::dir_copy(src, dest)
-  orderly2::orderly_init(..., root = dest)
+  fs::dir_copy(file.path(src, "src"), dest)
   invisible(dest)
 }

R/orderly.R

@@ -17,6 +17,7 @@
 ##' @examples
 ##' path <- orderly2::orderly_example("default")
 ##' orderly2::orderly_list_src(root = path)
+##' fs::dir_delete(path)
 orderly_list_src <- function(root = NULL) {
   root_path <- orderly_src_root(root)
   if (!file.exists(file.path(root_path, "src"))) {

R/run.R

@@ -150,6 +150,9 @@
 ##'
 ##' # and we can query the metadata:
 ##' orderly2::orderly_metadata_extract(name = "data", root = path)
+##'
+##' # Cleanup
+##' fs::dir_delete(path)
 orderly_run <- function(name, parameters = NULL, envir = NULL, echo = TRUE,
                         location = NULL, allow_remote = NULL,
                         pull_metadata = FALSE, search_options = NULL,

tests/testthat/test-example.R

@@ -1,18 +1,3 @@
-test_that("can use self destructing paths", {
-  res <- local({
-    res <- local({
-      tmp <- withr::local_tempfile()
-      path <- suppressMessages(orderly_example("default", dest = NULL))
-      list(path = path, exists_inner = file.exists(path))
-    })
-    res$exists_outer <- file.exists(res$path)
-    res
-  })
-  expect_true(res$exists_inner)
-  expect_false(res$exists_outer)
-})
-
-
 test_that("can use custom path", {
   path <- withr::local_tempfile()
   res <- suppressMessages(orderly_example("default", dest = path))
@@ -34,5 +19,5 @@ test_that("can set config", {
 test_that("error if path exists", {
   path <- withr::local_tempdir()
   expect_error(orderly_example("default", dest = path),
-               "The path '.+' cannot exist")
+               "The path '.+' must not exist")
 })