Merge pull request #183 from mrc-ide/mrc-5111

Drop `locate` argument everywhere public-facing
mrc-ide · Oct 18, 2024 · 1b65946 · 1b65946
2 parents 581a8e9 + be61222
commit 1b65946
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: orderly2
 Title: Orderly Next Generation
-Version: 1.99.42
+Version: 1.99.43
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Robert", "Ashton", role = "aut"),

diff --git a/R/cleanup.R b/R/cleanup.R
@@ -65,9 +65,8 @@
 ##'
 ##' # Do the actual deletion:
 ##' orderly2::orderly_cleanup("data", root = path)
-orderly_cleanup <- function(name = NULL, dry_run = FALSE, root = NULL,
-                            locate = TRUE) {
-  status <- orderly_cleanup_status(name, root, locate)
+orderly_cleanup <- function(name = NULL, dry_run = FALSE, root = NULL) {
+  status <- orderly_cleanup_status(name, root)
   n <- length(status$delete)
   if (n == 0) {
     cli::cli_alert_success("Nothing to clean")
@@ -93,7 +92,7 @@ orderly_cleanup <- function(name = NULL, dry_run = FALSE, root = NULL,
 
 ##' @export
 ##' @rdname orderly_cleanup
-orderly_cleanup_status <- function(name = NULL, root = NULL, locate = TRUE) {
+orderly_cleanup_status <- function(name = NULL, root = NULL) {
   p <- get_active_packet()
   is_active <- !is.null(p)
   if (is_active) {
@@ -107,7 +106,7 @@ orderly_cleanup_status <- function(name = NULL, root = NULL, locate = TRUE) {
     root_path <- detect_orderly_interactive_path(path)
     name <- basename(path)
   } else {
-    root_path <- orderly_src_root(root, locate, call = environment())
+    root_path <- orderly_src_root(root)
     if (is.null(name)) {
       ## This situation would be very odd, just disallow it
       cli::cli_abort("If 'root' is given explicitly, 'name' is required")

diff --git a/R/context.R b/R/context.R
@@ -62,7 +62,7 @@ orderly_run_info <- function() {
   id <- ctx$packet$id %||% NA_character_
   name <- ctx$name
 
-  root <- root_open(ctx$root, FALSE, TRUE, environment())
+  root <- root_open(ctx$root, require_orderly = TRUE)
 
   deps <- ctx$packet$depends
   deps_n <- vnapply(deps, function(x) nrow(x$files))

diff --git a/R/gitignore.R b/R/gitignore.R
@@ -33,8 +33,8 @@
 ##'
 ##' @return Nothing, called for its side effects
 ##' @export
-orderly_gitignore_update <- function(name, root = NULL, locate = TRUE) {
-  root_path <- orderly_src_root(root, locate, call = environment())
+orderly_gitignore_update <- function(name, root = NULL) {
+  root_path <- orderly_src_root(root)
   do_orderly_gitignore_update(name, root_path, environment())
 }
 

diff --git a/R/graph.R b/R/graph.R
@@ -1,7 +1,5 @@
-orderly_graph_packets <- function(from = NULL, to = NULL,
-                                  root = NULL, locate = FALSE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_graph_packets <- function(from = NULL, to = NULL, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   if (is.null(from) == is.null(to)) {
     cli::cli_abort("Exactly one of 'from' and 'to' must be given")
   }

diff --git a/R/location.R b/R/location.R
@@ -79,9 +79,8 @@
 ##'
 ##' @return Nothing
 ##' @export
-orderly_location_add <- function(name, type, args, root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_location_add <- function(name, type, args, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   assert_scalar_character(name, call = environment())
 
   if (name %in% location_reserved_name) {
@@ -95,7 +94,7 @@ orderly_location_add <- function(name, type, args, root = NULL, locate = TRUE) {
   loc <- new_location_entry(name, type, args, call = environment())
   if (type == "path") {
     assert_scalar_character(args$path, name = "path")
-    root_open(args$path, locate = FALSE, require_orderly = FALSE)
+    root_open(args$path, require_orderly = FALSE)
   } else if (type == "http") {
     assert_scalar_character(args$url, name = "url")
   } else if (type == "packit") {
@@ -174,9 +173,8 @@ orderly_location_add_packit <- function(name, url, token = NULL,
 ##'
 ##' @return Nothing
 ##' @export
-orderly_location_rename <- function(old, new, root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_location_rename <- function(old, new, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   assert_scalar_character(new, call = call)
 
   if (old %in% location_reserved_name) {
@@ -205,9 +203,8 @@ orderly_location_rename <- function(old, new, root = NULL, locate = TRUE) {
 ##'
 ##' @return Nothing
 ##' @export
-orderly_location_remove <- function(name, root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_location_remove <- function(name, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
 
   if (name %in% location_reserved_name) {
     cli::cli_abort("Cannot remove default location '{name}'")
@@ -261,9 +258,8 @@ orderly_location_remove <- function(name, root = NULL, locate = TRUE) {
 ##'   locations listed here.
 ##'
 ##' @export
-orderly_location_list <- function(verbose = FALSE, root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_location_list <- function(verbose = FALSE, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   if (verbose) {
     root$config$location
   } else {
@@ -289,10 +285,8 @@ orderly_location_list <- function(verbose = FALSE, root = NULL, locate = TRUE) {
 ##' @return Nothing
 ##'
 ##' @export
-orderly_location_pull_metadata <- function(location = NULL, root = NULL,
-                                           locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_location_pull_metadata <- function(location = NULL, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   location_name <- location_resolve_valid(location, root,
                                           include_local = FALSE,
                                           include_orphan = FALSE,
@@ -352,9 +346,8 @@ orderly_location_pull_metadata <- function(location = NULL, root = NULL,
 ##' @return Invisibly, the ids of packets that were pulled
 ##' @export
 orderly_location_pull_packet <- function(..., options = NULL, recursive = NULL,
-                                         root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+                                         root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   options <- as_orderly_search_options(options, list(allow_remote = TRUE))
   if (!options$allow_remote) {
     cli::cli_abort(
@@ -449,10 +442,8 @@ orderly_location_pull_packet <- function(..., options = NULL, recursive = NULL,
 ##'   known on the other location).
 ##'
 ##' @export
-orderly_location_push <- function(packet_id, location, root = NULL,
-                                  locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_location_push <- function(packet_id, location, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   location_name <- location_resolve_valid(location, root,
                                           include_local = FALSE,
                                           include_orphan = FALSE,

diff --git a/R/location_path.R b/R/location_path.R
@@ -7,7 +7,7 @@ orderly_location_path <- R6::R6Class(
 
   public = list(
     initialize = function(path) {
-      private$root <- root_open(path, locate = FALSE, require_orderly = FALSE)
+      private$root <- root_open(path, require_orderly = FALSE)
     },
 
     list = function() {

diff --git a/R/orderly.R b/R/orderly.R
@@ -17,8 +17,8 @@
 ##' @examples
 ##' path <- orderly2::orderly_example("default")
 ##' orderly2::orderly_list_src(root = path)
-orderly_list_src <- function(root = NULL, locate = TRUE) {
-  root_path <- orderly_src_root(root, locate)
+orderly_list_src <- function(root = NULL) {
+  root_path <- orderly_src_root(root)
   if (!file.exists(file.path(root_path, "src"))) {
     return(character())
   }
@@ -51,9 +51,8 @@ orderly_list_src <- function(root = NULL, locate = TRUE) {
 ##'
 ##' @return Nothing, called for its side effects only
 ##' @export
-orderly_new <- function(name, template = NULL, force = FALSE,
-                        root = NULL, locate = TRUE) {
-  root <- root_open(root, locate, require_orderly = TRUE, call = environment())
+orderly_new <- function(name, template = NULL, force = FALSE, root = NULL) {
+  root <- root_open(root, require_orderly = TRUE)
   dest <- file.path(root$path, "src", name)
   existing_entrypoint_filename <- find_entrypoint_filename(
     dest, suppress_zero_files = TRUE

diff --git a/R/outpack_checksum.R b/R/outpack_checksum.R
@@ -2,7 +2,7 @@
 ## present. It might have been intended for the R-backed server, now
 ## defunct?
 outpack_checksum <- function(hash_algorithm = NULL, root = NULL) {
-  root <- root_open(root, locate = TRUE, require_orderly = FALSE)
+  root <- root_open(root, require_orderly = FALSE)
   hash_algorithm <- hash_algorithm %||% root$config$core$hash_algorithm
 
   ## Don't use the index ever here; we want to always read this from

diff --git a/R/outpack_config.R b/R/outpack_config.R
@@ -39,10 +39,8 @@
 ##'                              core.path_archive = NULL,
 ##'                              root = path)
 ##' fs::dir_tree(path, all = TRUE)
-orderly_config_set <- function(..., options = list(...), root = NULL,
-                               locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_config_set <- function(..., options = list(...), root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   if (!missing(options) && ...length() > 0) {
     stop("If 'options' is given, no dot arguments are allowed")
   }
@@ -111,9 +109,8 @@ orderly_config_set <- function(..., options = list(...), root = NULL,
 ##' path <- withr::local_tempdir()
 ##' orderly2::orderly_init(path)
 ##' orderly2::orderly_config(path)
-orderly_config <- function(root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_config <- function(root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   root$config
 }
 

diff --git a/R/outpack_hash.R b/R/outpack_hash.R
@@ -21,11 +21,9 @@
 ##' @export
 ##' @examples
 ##' orderly2::orderly_hash_data("hello", "md5")
-orderly_hash_file <- function(path, algorithm = NULL, root = NULL,
-                              locate = TRUE) {
+orderly_hash_file <- function(path, algorithm = NULL, root = NULL) {
   if (is.null(algorithm)) {
-    root <- root_open(root, locate = locate, require_orderly = FALSE,
-                      call = environment())
+    root <- root_open(root, require_orderly = FALSE)
     algorithm <- root$config$core$hash_algorithm
   }
   hash_file(path, algorithm, call = environment())
@@ -35,11 +33,9 @@ orderly_hash_file <- function(path, algorithm = NULL, root = NULL,
 ##' @param data A string to hash
 ##' @export
 ##' @rdname orderly_hash
-orderly_hash_data <- function(data, algorithm = NULL, root = NULL,
-                              locate = TRUE) {
+orderly_hash_data <- function(data, algorithm = NULL, root = NULL) {
   if (is.null(algorithm)) {
-    root <- root_open(root, locate = locate, require_orderly = FALSE,
-                      call = environment())
+    root <- root_open(root, require_orderly = FALSE)
     algorithm <- root$config$core$hash_algorithm
   }
   hash_data(data, algorithm, call = call)

diff --git a/R/outpack_helpers.R b/R/outpack_helpers.R
@@ -81,9 +81,8 @@
 ##' @export
 orderly_copy_files <- function(..., files, dest, overwrite = TRUE,
                                envir = parent.frame(), options = NULL,
-                               root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+                               root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
 
   ## Validate files and dest early; it gives a better error where this
   ## was not provided with names.

diff --git a/R/outpack_metadata.R b/R/outpack_metadata.R
@@ -8,25 +8,18 @@
 ##'   this id is not known
 ##'
 ##' @param root The path to the root directory, or `NULL` (the
-##'   default) to search for one from the current working directory if
-##'   `locate` is `TRUE`. This function does not require that the
-##'   directory is configured for orderly, and can be any `outpack`
-##'   root (see [orderly2::orderly_init] for details).
-##'
-##' @param locate Logical, indicating if the root should be searched
-##'   for.  If `TRUE`, then we looks in the directory given for `root`
-##'   (or the working directory if `NULL`) and then up through its
-##'   parents until it finds an `.outpack` directory or
-##'   `orderly_config.yml`
+##'   default) to search for one from the current working
+##'   directory. This function does not require that the directory is
+##'   configured for orderly, and can be any `outpack` root (see
+##'   [orderly2::orderly_init] for details).
 ##'
 ##' @return A list of metadata. See the outpack schema for details
 ##'   (https://github.com/mrc-ide/outpack)
 ##'
 ##' @export
-orderly_metadata <- function(id, root = NULL, locate = FALSE) {
+orderly_metadata <- function(id, root = NULL) {
   validate_outpack_id(id, call = environment())
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+  root <- root_open(root, require_orderly = FALSE)
   path_metadata <- file.path(root$path, ".outpack", "metadata", id)
   if (!file.exists(path_metadata)) {
     cli::cli_abort("Packet '{id}' not found in outpack index")

diff --git a/R/outpack_packet.R b/R/outpack_packet.R
@@ -23,7 +23,7 @@
 ##' @noRd
 outpack_packet_start <- function(path, name, parameters = NULL, id = NULL,
                                  root = NULL) {
-  root <- root_open(root, locate = FALSE, require_orderly = FALSE)
+  root <- root_open(root, require_orderly = FALSE)
 
   assert_scalar_character(name)
   assert_is_directory(path)

diff --git a/R/outpack_tools.R b/R/outpack_tools.R
@@ -197,10 +197,8 @@
 ##'   names of `extract`; see Details for more information.
 ##'
 ##' @export
-orderly_metadata_extract <- function(..., extract = NULL, root = NULL,
-                                     locate = TRUE) {
-  root <- root_open(root, locate = locate, require_orderly = FALSE,
-                    call = environment())
+orderly_metadata_extract <- function(..., extract = NULL, root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   if (dots_is_literal_id(...)) {
     ids <- ..1
   } else {

diff --git a/R/prune.R b/R/prune.R
@@ -22,8 +22,8 @@
 ##'
 ##' @return Invisibly, a character vector of orphaned packet ids
 ##' @export
-orderly_prune_orphans <- function(root = NULL, locate = TRUE) {
-  root <- root_open(root, locate = TRUE, require_orderly = FALSE)
+orderly_prune_orphans <- function(root = NULL) {
+  root <- root_open(root, require_orderly = FALSE)
   id <- root$index$location("orphan")$packet
   if (length(id) == 0) {
     return(invisible(id))

diff --git a/R/query_explain.R b/R/query_explain.R
@@ -16,7 +16,7 @@
 orderly_query_explain <- function(..., parameters = NULL,
                                   envir = parent.frame(),
                                   options = NULL, root = NULL) {
-  root <- root_open(root, locate = TRUE, require_orderly = FALSE)
+  root <- root_open(root, require_orderly = FALSE)
   query <- as_orderly_query(...)
   options <- as_orderly_search_options(options)
   found <- orderly_search(query, parameters = parameters, envir = envir,

diff --git a/R/query_index.R b/R/query_index.R
@@ -84,7 +84,7 @@ query_index <- R6::R6Class(
 ## help with the pulling metadata issue (as we could then control only
 ## pulling once in a session).
 new_query_index <- function(root, options) {
-  root <- root_open(root, locate = FALSE, require_orderly = FALSE)
+  root <- root_open(root, require_orderly = FALSE)
 
   if (options$pull_metadata) {
     orderly_location_pull_metadata(options$location, root)

diff --git a/R/query_search.R b/R/query_search.R
@@ -33,7 +33,7 @@
 ##' @export
 orderly_search <- function(..., parameters = NULL, envir = parent.frame(),
                            options = NULL, root = NULL) {
-  root <- root_open(root, locate = TRUE, require_orderly = FALSE)
+  root <- root_open(root, require_orderly = FALSE)
   query <- as_orderly_query(...)
   options <- as_orderly_search_options(options)
   validate_parameters(parameters, environment())