From aa33d54511954748eeb1e32868266e14a467f7ef Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Tue, 22 Oct 2024 09:59:01 +0100
Subject: [PATCH] Make example runner less clever

---
 R/cleanup.R             | 13 ++++++++-----
 R/example.R             | 16 +++++++++-------
 R/orderly.R             |  1 +
 R/run.R                 |  3 +++
 man/orderly_cleanup.Rd  | 13 ++++++++-----
 man/orderly_example.Rd  |  2 ++
 man/orderly_list_src.Rd |  1 +
 man/orderly_run.Rd      |  3 +++
 8 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/R/cleanup.R b/R/cleanup.R
index 41026a37..a325a939 100644
--- a/R/cleanup.R
+++ b/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.
@@ -42,6 +42,7 @@
 ##'
 ##' @export
 ##' @examples
+##' message(sprintf("Running in %s", format(environment())))
 ##' # Create a simple example:
 ##' path <- orderly2::orderly_example("default")
 ##'
@@ -65,6 +66,8 @@
 ##'
 ##' # Do the actual deletion:
 ##' orderly2::orderly_cleanup("data", root = path)
+##'
+##' unlink(path, recursive = TRUE)
 orderly_cleanup <- function(name = NULL, dry_run = FALSE, root = NULL) {
   status <- orderly_cleanup_status(name, root)
   n <- length(status$delete)
diff --git a/R/example.R b/R/example.R
index 34c9cbe1..21b94faa 100644
--- a/R/example.R
+++ b/R/example.R
@@ -19,18 +19,20 @@
 ##' @examples
 ##' path <- orderly2::orderly_example("default")
 ##' orderly2::orderly_list_src(root = path)
+##'
+##' unlink(path, recursive = TRUE)
 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}' cannot 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)
 }
diff --git a/R/orderly.R b/R/orderly.R
index 67058364..a021eb42 100644
--- a/R/orderly.R
+++ b/R/orderly.R
@@ -17,6 +17,7 @@
 ##' @examples
 ##' path <- orderly2::orderly_example("default")
 ##' orderly2::orderly_list_src(root = path)
+##' unlink(path, recursive = TRUE)
 orderly_list_src <- function(root = NULL) {
   root_path <- orderly_src_root(root)
   if (!file.exists(file.path(root_path, "src"))) {
diff --git a/R/run.R b/R/run.R
index b7af6c81..b02d7dcc 100644
--- a/R/run.R
+++ b/R/run.R
@@ -150,6 +150,9 @@
 ##'
 ##' # and we can query the metadata:
 ##' orderly2::orderly_metadata_extract(name = "data", root = path)
+##'
+##' # Cleanup
+##' unlink(path, recursive = TRUE)
 orderly_run <- function(name, parameters = NULL, envir = NULL, echo = TRUE,
                         location = NULL, allow_remote = NULL,
                         pull_metadata = FALSE, search_options = NULL,
diff --git a/man/orderly_cleanup.Rd b/man/orderly_cleanup.Rd
index b6ebb33a..32edb972 100644
--- a/man/orderly_cleanup.Rd
+++ b/man/orderly_cleanup.Rd
@@ -41,11 +41,11 @@ After file deletion, we look through and remove all empty
 directories; orderly2 has similar semantics here to git where
 directories are never directly tracked.
 
-For recent \code{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 \code{.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 \code{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 \code{.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.
@@ -60,6 +60,7 @@ files then compare that with the directory.
 }
 
 \examples{
+message(sprintf("Running in \%s", format(environment())))
 # Create a simple example:
 path <- orderly2::orderly_example("default")
 
@@ -83,4 +84,6 @@ orderly2::orderly_cleanup_status("data", root = path)
 
 # Do the actual deletion:
 orderly2::orderly_cleanup("data", root = path)
+
+unlink(path, recursive = TRUE)
 }
diff --git a/man/orderly_example.Rd b/man/orderly_example.Rd
index b6ce6d1f..c1d6439a 100644
--- a/man/orderly_example.Rd
+++ b/man/orderly_example.Rd
@@ -28,4 +28,6 @@ should not form part of your workflow!
 \examples{
 path <- orderly2::orderly_example("default")
 orderly2::orderly_list_src(root = path)
+
+unlink(path, recursive = TRUE)
 }
diff --git a/man/orderly_list_src.Rd b/man/orderly_list_src.Rd
index 214e0439..1cfcabb9 100644
--- a/man/orderly_list_src.Rd
+++ b/man/orderly_list_src.Rd
@@ -26,6 +26,7 @@ as the directory (e.g., \code{src/data/data.R} corresponds to \code{data}).
 \examples{
 path <- orderly2::orderly_example("default")
 orderly2::orderly_list_src(root = path)
+unlink(path, recursive = TRUE)
 }
 \seealso{
 \link{orderly_metadata_extract} for listing packets
diff --git a/man/orderly_run.Rd b/man/orderly_run.Rd
index 5173ee82..6171a683 100644
--- a/man/orderly_run.Rd
+++ b/man/orderly_run.Rd
@@ -197,4 +197,7 @@ fs::dir_tree(path)
 
 # and we can query the metadata:
 orderly2::orderly_metadata_extract(name = "data", root = path)
+
+# Cleanup
+unlink(path, recursive = TRUE)
 }