Rename arguments

mrc-ide · Oct 24, 2024 · edb6e2e · edb6e2e
1 parent 9ddcc1d
commit edb6e2e
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Showing 29 changed files with 119 additions and 87 deletions.
diff --git a/R/compare.R b/R/compare.R
@@ -41,17 +41,17 @@ compare_filesets <- function(target, current) {
 orderly_compare_packets <- function(target, current,
                                     location = NULL,
                                     allow_remote = NULL,
-                                    pull_metadata = FALSE,
+                                    fetch_metadata = FALSE,
                                     root = NULL) {
   root <- root_open(root, require_orderly = FALSE)
   validate_outpack_id(target, call = environment())
   validate_outpack_id(current, call = environment())
 
   options <- build_search_options(location = location,
                                   allow_remote = allow_remote,
-                                  pull_metadata = pull_metadata)
+                                  fetch_metadata = fetch_metadata)
 
-  if (options$pull_metadata) {
+  if (options$fetch_metadata) {
     orderly_location_fetch_metadata(options$location, root = root)
   }
 
@@ -115,7 +115,7 @@ compare_file_contents <- function(cmp, files) {
   # very straightforward, and covers the case where the file only exists
   # remotely transparent.
   #
-  # pull_metadata is intentionally hardcoded to FALSE, regardless of what the
+  # fetch_metadata is intentionally hardcoded to FALSE, regardless of what the
   # user may have specified as an argument to orderly_compare_packets: the
   # latter would have already pulled the files once, and we don't need to do it
   # again.
@@ -124,15 +124,15 @@ compare_file_contents <- function(cmp, files) {
                      files = files,
                      location = cmp$search_options$location,
                      allow_remote = cmp$search_options$allow_remote,
-                     pull_metadata = FALSE,
+                     fetch_metadata = FALSE,
                      root = cmp$root)
 
   orderly_copy_files(cmp$current$id,
                      dest = path_current,
                      files = files,
                      location = cmp$search_options$location,
                      allow_remote = cmp$search_options$allow_remote,
-                     pull_metadata = FALSE,
+                     fetch_metadata = FALSE,
                      root = cmp$root)
 
 

diff --git a/R/interactive.R b/R/interactive.R
@@ -81,10 +81,10 @@ detect_orderly_interactive_path <- function(
 ##' @export
 orderly_interactive_set_search_options <- function(location = NULL,
                                                    allow_remote = NULL,
-                                                   pull_metadata = FALSE) {
+                                                   fetch_metadata = FALSE) {
   options <- build_search_options(location = location,
                                   allow_remote = allow_remote,
-                                  pull_metadata = pull_metadata)
+                                  fetch_metadata = fetch_metadata)
   .interactive$search_options <- options
 }
 

diff --git a/R/location.R b/R/location.R
@@ -396,7 +396,7 @@ orderly_location_pull_metadata <- function(...) {
 orderly_location_pull <- function(expr,
                                   name = NULL,
                                   location = NULL,
-                                  pull_metadata = FALSE,
+                                  fetch_metadata = FALSE,
                                   recursive = NULL,
                                   options = NULL,
                                   root = NULL) {
@@ -410,14 +410,14 @@ orderly_location_pull <- function(expr,
                           name = name,
                           location = location,
                           allow_remote = TRUE,
-                          pull_metadata = pull_metadata,
+                          fetch_metadata = fetch_metadata,
                           root = root)
   }
 
   if (length(ids) == 0 || (length(ids) == 1 && is.na(ids))) {
-    if (!pull_metadata) {
+    if (!fetch_metadata) {
       hint <- c(i = paste("Did you forget to pull metadata? You can do this",
-                          "by using the argument {.code pull_metadata = TRUE}",
+                          "by using the argument {.code fetch_metadata = TRUE}",
                           "in the call to 'orderly_location_pull()', or",
                           "by running 'orderly_location_fetch_metadata()'"))
     } else {

diff --git a/R/metadata.R b/R/metadata.R
@@ -305,7 +305,7 @@ orderly_dependency <- function(name, query, files) {
       parameters = ctx$parameters,
       location = search_options$location,
       allow_remote = search_options$allow_remote,
-      pull_metadata = search_options$pull_metadata,
+      fetch_metadata = search_options$fetch_metadata,
       envir = ctx$envir,
       root = ctx$root)
   }

diff --git a/R/outpack_helpers.R b/R/outpack_helpers.R
@@ -82,7 +82,7 @@
 ##' @export
 orderly_copy_files <- function(expr, files, dest, overwrite = TRUE,
                                name = NULL, location = NULL,
-                               allow_remote = NULL, pull_metadata = FALSE,
+                               allow_remote = NULL, fetch_metadata = FALSE,
                                parameters = NULL, options = NULL,
                                envir = parent.frame(),
                                root = NULL) {
@@ -92,7 +92,7 @@ orderly_copy_files <- function(expr, files, dest, overwrite = TRUE,
   ## allow_remote later in error messages.
   options <- build_search_options(location = location,
                                   allow_remote = allow_remote,
-                                  pull_metadata = pull_metadata)
+                                  fetch_metadata = fetch_metadata)
 
   ## Validate files and dest early; it gives a better error where this
   ## was not provided with names.
@@ -112,7 +112,7 @@ orderly_copy_files <- function(expr, files, dest, overwrite = TRUE,
                          parameters = parameters,
                          location = options$location,
                          allow_remote = options$allow_remote,
-                         pull_metadata = options$pull_metadata,
+                         fetch_metadata = options$fetch_metadata,
                          root = root)
     if (length(id) > 1) {
       cli::cli_abort(

diff --git a/R/outpack_packet.R b/R/outpack_packet.R
@@ -177,7 +177,7 @@ outpack_packet_use_dependency <- function(packet, query, files,
                        envir = envir,
                        location = search_options$location,
                        allow_remote = search_options$allow_remote,
-                       pull_metadata = search_options$pull_metadata,
+                       fetch_metadata = search_options$fetch_metadata,
                        root = packet$root)
   if (is.na(id)) {
     explanation <- orderly_query_explain(
@@ -201,7 +201,7 @@ outpack_packet_use_dependency <- function(packet, query, files,
   result <- orderly_copy_files(id, files = files, dest = packet$path,
                                location = search_options$location,
                                allow_remote = search_options$allow_remote,
-                               pull_metadata = search_options$pull_metadata,
+                               fetch_metadata = search_options$fetch_metadata,
                                overwrite = overwrite,
                                envir = envir,
                                root = packet$root)

diff --git a/R/outpack_tools.R b/R/outpack_tools.R
@@ -198,7 +198,8 @@
 ##'
 ##' @export
 orderly_metadata_extract <- function(expr = NULL, name = NULL, location = NULL,
-                                     allow_remote = NULL, pull_metadata = FALSE,
+                                     allow_remote = NULL,
+                                     fetch_metadata = FALSE,
                                      extract = NULL, options = NULL,
                                      root = NULL) {
   root <- root_open(root, require_orderly = FALSE)
@@ -211,7 +212,7 @@ orderly_metadata_extract <- function(expr = NULL, name = NULL, location = NULL,
                           name = name,
                           location = location,
                           allow_remote = allow_remote,
-                          pull_metadata = pull_metadata,
+                          fetch_metadata = fetch_metadata,
                           root = root)
   }
   extract <- parse_extract(extract, environment())

diff --git a/R/query_explain.R b/R/query_explain.R
@@ -25,7 +25,7 @@ orderly_query_explain <- function(expr, name = NULL, scope = NULL,
   found <- orderly_search(query, parameters = parameters, envir = envir,
                           location = location,
                           allow_remote = allow_remote,
-                          pull_metadata = FALSE,
+                          fetch_metadata = FALSE,
                           root = root)
   query_simplified <- query_simplify(query)
   ret <- list(found = found,
@@ -40,7 +40,7 @@ orderly_query_explain <- function(expr, name = NULL, scope = NULL,
                             envir = envir,
                             location = location,
                             allow_remote = allow_remote,
-                            pull_metadata = FALSE,
+                            fetch_metadata = FALSE,
                             root = root)
     ret$parts[[name]] <- list(
       name = name,

diff --git a/R/query_index.R b/R/query_index.R
@@ -86,7 +86,7 @@ query_index <- R6::R6Class(
 new_query_index <- function(root, options) {
   root <- root_open(root, require_orderly = FALSE)
 
-  if (options$pull_metadata) {
+  if (options$fetch_metadata) {
     orderly_location_fetch_metadata(options$location, root = root)
   }
   idx <- root$index$data()

diff --git a/R/query_search.R b/R/query_search.R
@@ -21,7 +21,7 @@
 ##'
 ##' @param options **DEPRECATED**. Please don't use this any more, and
 ##'   instead use the arguments `location`, `allow_remote` and
-##'   `pull_metadata` directly.
+##'   `fetch_metadata` directly.
 ##'
 ##' @return A character vector of matching ids. In the case of no
 ##'   match from a query returning a single value (e.g., `latest(...)`
@@ -32,14 +32,14 @@
 orderly_search <- function(expr, name = NULL, scope = NULL, subquery = NULL,
                            parameters = NULL, envir = parent.frame(),
                            location = NULL, allow_remote = NULL,
-                           pull_metadata = FALSE, options = NULL,
+                           fetch_metadata = FALSE, options = NULL,
                            root = NULL) {
   root <- root_open(root, require_orderly = FALSE)
   compatibility_fix_options(options, "orderly_search")
   query <- as_orderly_query(expr, name, scope, subquery)
   options <- build_search_options(location = location,
                                   allow_remote = allow_remote,
-                                  pull_metadata = pull_metadata)
+                                  fetch_metadata = fetch_metadata)
   validate_parameters(parameters, environment())
   orderly_query_eval(query, parameters, envir, options, root,
                      call = environment())
@@ -64,9 +64,9 @@ orderly_search <- function(expr, name = NULL, scope = NULL, subquery = NULL,
 ##'   you might pull a large quantity of data.  The default is `NULL`. This is
 ##'   `TRUE` if remote locations are listed explicitly as a character
 ##'   vector in the `location` argument, or if you have specified
-##'   `pull_metadata = TRUE`, otherwise `FALSE`.
+##'   `fetch_metadata = TRUE`, otherwise `FALSE`.
 ##'
-##' @param pull_metadata Logical, indicating if we should pull
+##' @param fetch_metadata Logical, indicating if we should pull
 ##'   metadata immediately before the search. If `location` is given,
 ##'   then we will pass this through to
 ##'   [orderly2::orderly_location_fetch_metadata] to filter locations
@@ -76,7 +76,7 @@ orderly_search <- function(expr, name = NULL, scope = NULL, subquery = NULL,
 ##'   needlessly slow.
 ##'
 ##' @return An object of class `orderly_search_options` which should
-##'   not be modified after creation (but see note about `pull_metadata`)
+##'   not be modified after creation (but see note about `fetch_metadata`)
 ##'
 ##' @export
 orderly_search_options <- function(location = NULL,
@@ -85,7 +85,8 @@ orderly_search_options <- function(location = NULL,
   cli::cli_warn(
     c("Use of 'orderly_search_options' is deprecated",
       i = paste("You should just pass these arguments directly into functions",
-                "that previously accepted 'options'")),
+                "that previously accepted 'options'"),
+      i = "Please note that 'pull_metadata' has become 'fetch_metadata'"),
     .frequency = "regularly",
     .frequency_id = "orderly_search_options")
   build_search_options(location, allow_remote, pull_metadata)
@@ -99,7 +100,7 @@ compatibility_fix_options <- function(options, name,
     cli::cli_warn(
       c("Use of '{arg}' in '{name}()' is deprecated and will be removed soon",
         i = paste("Please pass the arguments to options ('location',",
-                  "'allow_remote' and 'pull_metadata') directly to '{name}'"),
+                  "'allow_remote' and 'fetch_metadata') directly to '{name}'"),
         "!" = paste("If you have {.strong also} passed these options in",
                     "to your function I am about to silently overwrite them")),
       .frequency = "regularly",
@@ -111,22 +112,23 @@ compatibility_fix_options <- function(options, name,
 
 
 build_search_options <- function(location = NULL, allow_remote = NULL,
-                                 pull_metadata = FALSE, call = parent.frame()) {
+                                 fetch_metadata = FALSE,
+                                 call = parent.frame()) {
   if (!is.null(location)) {
     assert_character(location, call = call)
   }
   has_remote_location <- !is.null(location) &&
     length(setdiff(location, c("local", "orphan")) > 0)
 
-  assert_scalar_logical(pull_metadata, call = call)
+  assert_scalar_logical(fetch_metadata, call = call)
   if (is.null(allow_remote)) {
-    allow_remote <- has_remote_location || pull_metadata
+    allow_remote <- has_remote_location || fetch_metadata
   } else {
     assert_scalar_logical(allow_remote, call = call)
   }
   ret <- list(location = location,
               allow_remote = allow_remote,
-              pull_metadata = pull_metadata)
+              fetch_metadata = fetch_metadata)
   class(ret) <- "orderly_search_options"
   ret
 }

diff --git a/R/run.R b/R/run.R
@@ -35,7 +35,7 @@
 ##'
 ##' @section Which packets might be selected from locations?:
 ##'
-##' The arguments `location`, `allow_remote` and `pull_metadata`
+##' The arguments `location`, `allow_remote` and `fetch_metadata`
 ##'   control where outpack searches for packets with the given query
 ##'   and if anything might be moved over the network (or from one
 ##'   outpack archive to another). By default everything is resolved
@@ -48,7 +48,7 @@
 ##'   same content anywhere else in an unpacked packet we will reuse
 ##'   the same content without re-fetching.
 ##'
-##' If `pull_metadata = TRUE`, then we will refresh location metadata
+##' If `fetch_metadata = TRUE`, then we will refresh location metadata
 ##'   before pulling, and the `location` argument controls which
 ##'   locations are pulled from.
 ##'
@@ -68,7 +68,7 @@
 ##'   as they currently exist on production right now with the options:
 ##'
 ##' ```
-##' location = "production", pull_metadata = TRUE
+##' location = "production", fetch_metadata = TRUE
 ##' ```
 ##'
 ##' which updates your current metadata from production, then runs
@@ -127,7 +127,7 @@
 ##'
 ##' @param search_options **DEPRECATED**. Please don't use this any
 ##'   more, and instead use the arguments `location`, `allow_remote`
-##'   and `pull_metadata` directly.
+##'   and `fetch_metadata` directly.
 ##'
 ##' @param root The path to the root directory, or `NULL` (the
 ##'   default) to search for one from the current working
@@ -155,7 +155,7 @@
 ##' 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,
+                        fetch_metadata = FALSE, search_options = NULL,
                         root = NULL) {
   env_root_src <- Sys.getenv("ORDERLY_SRC_ROOT", NA_character_)
   root <- root_open(root, require_orderly = is.na(env_root_src),
@@ -181,7 +181,7 @@ orderly_run <- function(name, parameters = NULL, envir = NULL, echo = TRUE,
 
   search_options <- build_search_options(location = location,
                                          allow_remote = allow_remote,
-                                         pull_metadata = pull_metadata)
+                                         fetch_metadata = fetch_metadata)
 
   id <- outpack_id()
   path <- file.path(root_src, "draft", name, id)

diff --git a/R/validate.R b/R/validate.R
@@ -57,7 +57,7 @@ orderly_validate_archive <- function(expr = NULL, name = NULL,
                           name = name,
                           location = "local",
                           allow_remote = FALSE,
-                          pull_metadata = FALSE,
+                          fetch_metadata = FALSE,
                           root = root)
   }
 

diff --git a/man/orderly_compare_packets.Rd b/man/orderly_compare_packets.Rd
diff --git a/man/orderly_copy_files.Rd b/man/orderly_copy_files.Rd