sketch #1317

DESCRIPTION

@@ -12,7 +12,7 @@ Description: Pipeline tools coordinate the pieces of computationally
   The methodology in this package
   borrows from GNU 'Make' (2015, ISBN:978-9881443519)
   and 'drake' (2018, <doi:10.21105/joss.00550>).
-Version: 1.8.0.9013
+Version: 1.8.0.9014
 License: MIT + file LICENSE
 URL: https://docs.ropensci.org/targets/, https://github.com/ropensci/targets
 BugReports: https://github.com/ropensci/targets/issues
@@ -97,7 +97,7 @@ Suggests:
   paws.storage (>= 0.4.0),
   pkgload (>= 1.1.0),
   processx (>= 3.4.3),
-  qs (>= 0.24.1),
+  qs2,
   reprex (>= 2.0.0),
   rstudioapi (>= 0.11),
   R.utils (>= 2.6.0),

NEWS.md

@@ -1,4 +1,4 @@
-# targets 1.8.0.9013 (development)
+# targets 1.8.0.9014 (development)
 
 * Un-break workflows that use `format = "file_fast"` (#1339, @koefoeden).
 * Fix deadlock in `error = "trim"` (#1340, @koefoeden).
@@ -19,6 +19,7 @@
 * Omit whole stem targets from branch subpipelines when `retrieval` is `"main"` and only a bud is actually used. The same cannot be done with branches because each branch may need to be (un)marshaled individually.
 * Compress branches into references when `retrieval` is `"worker"` and the whole pattern is part of the subpipeline.
 * Avoid duplicated branch aggregation: just send the branches over the network.
+* Back-compatibly switch `format = "qs"` from `qs` to `qs2` (#1373).
 
 # targets 1.8.0
 

R/class_qs.R

@@ -11,18 +11,37 @@ store_assert_format_setting.qs <- function(format) {
 
 #' @export
 store_read_path.tar_qs <- function(store, path) {
-  qs::qread(file = path, use_alt_rep = TRUE)
+  tryCatch(
+    qs2::qs_read(
+      file = path,
+      validate_checksum = FALSE,
+      nthreads = store$resources$qs$nthreads %|||% 1L
+    ),
+    # nocov start
+    error = function(condition) {
+      getNamespace("qs")$qread(
+        file = path,
+        use_alt_rep = TRUE,
+        nthreads = store$resources$qs$nthreads %|||% 1L
+      )
+    }
+    # nocov end
+  )
 }
 
 #' @export
 store_write_path.tar_qs <- function(store, object, path) {
-  preset <- store$resources$qs$preset %|||%
-    store$resources$preset %|||%
-    "high"
-  qs::qsave(x = object, file = path, preset = preset)
+  qs2::qs_save(
+    object = object,
+    file = path,
+    preset = preset,
+    compress_level = store$resources$qs$compress_level %|||% 3L,
+    shuffle = store$resources$qs$shuffle %|||% TRUE,
+    nthreads = store$resources$qs$nthreads %|||% 1L
+  )
 }
 
 #' @export
 store_get_packages.tar_qs <- function(store) {
-  "qs"
+  "qs2"
 }

R/class_resources_qs.R

@@ -1,25 +1,40 @@
 resources_qs_init <- function(
-  preset = "high"
+  compress_level = 3L,
+  shuffle = TRUE,
+  nthreads = 1L
 ) {
   resources_qs_new(
-    preset = preset
+    compress_level = compress_level,
+    shuffle = shuffle,
+    nthreads = nthreads
   )
 }
 
 resources_qs_new <- function(
-  preset = NULL
+  compress_level = NULL,
+  shuffle = NULL,
+  nthreads = NULL
 ) {
   out <- new.env(parent = emptyenv(), hash = FALSE)
-  out$preset <- preset
+  out$compress_level <- compress_level
+  out$shuffle <- shuffle
+  out$nthreads <- nthreads
   enclass(out, resources_qs_s3_class)
 }
 
 resources_qs_s3_class <- c("tar_resources_qs", "tar_resources")
 
 #' @export
 resources_validate.tar_resources_qs <- function(resources) {
-  tar_assert_scalar(resources$preset)
-  tar_assert_chr(resources$preset)
+  for (field in c("compress_level", "nthreads")) {
+    tar_assert_scalar(resources[[field]])
+    tar_assert_int(resources[[field]])
+    tar_assert_finite(resources[[field]])
+    tar_assert_none_na(resources[[field]])
+  }
+  tar_assert_scalar(resources$shuffle)
+  tar_assert_lgl(resources$shuffle)
+  tar_assert_none_na(resources$shuffle)
 }
 
 #' @export

R/tar_resources.R

@@ -91,9 +91,8 @@
 #'   Applies to all formats ending with the `"_parquet"` suffix.
 #'   For details on formats, see the `format` argument of [tar_target()].
 #' @param qs Output of function `tar_resources_qs()`.
-#'   Non-default arguments to `qs::qread()` and
-#'   `qs::qsave()` for `qs`-based storage formats.
-#'   Applies to all formats ending with the `"_qs"` suffix.
+#'   Non-default arguments to `qs2::qs_read()` and
+#'   `qs2::qs_save()` for targets with `format = "qs"`.
 #'   For details on formats, see the `format` argument of [tar_target()].
 #' @param repository_cas Output of function [tar_resources_repository_cas()]
 #'   with configuration details for [tar_repository_cas()] storage

R/tar_resources_qs.R

@@ -8,8 +8,15 @@
 #' @inheritSection tar_resources Resources
 #' @return Object of class `"tar_resources_qs"`, to be supplied
 #'   to the qs argument of `tar_resources()`.
-#' @param preset Character of length 1, `preset`
-#'   argument of `qs::qsave()`. Defaults to `"high"`.
+#' @param compress_level Positive integer, `compress_level` argument of
+#'   [qs2::qs_save()] to control the compression level.
+#' @param shuffle `TRUE` to use byte shuffling in
+#'   [qs2::qs_save()] to improve compression at the cost of some
+#'   computation time, `FALSE` to forgo byte shuffling.
+#' @param nthreads Positive integer, number of threads to use for
+#'   functions in the `qs2` package to save and read the data.
+#' @param preset Deprecated in `targets` version 1.8.0.9014 (2024-11-11)
+#'   and not used.
 #' @examples
 #' # Somewhere in you target script file (usually _targets.R):
 #' tar_target(
@@ -21,11 +28,15 @@
 #'   )
 #' )
 tar_resources_qs <- function(
-  preset = targets::tar_option_get("resources")$qs$preset
+  compress_level = targets::tar_option_get("resources")$qs$compress_level,
+  shuffle = targets::tar_option_get("resources")$qs$shuffle,
+  nthreads = targets::tar_option_get("resources")$qs$nthreads,
+  preset = NULL
 ) {
-  preset <- preset %|||% "high"
   out <- resources_qs_init(
-    preset = preset
+    compress_level = compress_level %|||% 3L,
+    shuffle = shuffle %|||% TRUE,
+    nthreads = nthreads %|||% 1L
   )
   resources_validate(out)
   out

R/tar_target.R

@@ -47,9 +47,15 @@
 #'     existing files (and/or directories), then the format becomes
 #'     `"file"` before [tar_make()] saves the target. Otherwise,
 #'     the format becomes `"qs"`.
-#'   * `"qs"`: Uses `qs::qsave()` and `qs::qread()`. Should work for
-#'     most objects, much faster than `"rds"`. Optionally set the
-#'     preset for `qsave()` through `tar_resources()` and `tar_resources_qs()`.
+#'   * `"qs"`: Uses `qs2::qs_save()` and `qs2::qs_read()`. Should work for
+#'     most objects, much faster than `"rds"`. Optionally configure settings
+#'     through `tar_resources()` and `tar_resources_qs()`.
+#'
+#'     Prior to `targets` version 1.8.0.9014, `format = "qs"` used the `qs`
+#'     package. `qs` has since been superseded in favor of `qs2`, and so
+#'     later versions of `targets` use `qs2` to save new data. To read
+#'     existing data, `targets` first attempts [qs2::qs_read()], and then if
+#'     that fails, it falls back on [qs::qread()].
 #'   * `"feather"`: Uses `arrow::write_feather()` and
 #'     `arrow::read_feather()` (version 2.0). Much faster than `"rds"`,
 #'     but the value must be a data frame. Optionally set

tests/testthat/test-class_resources_qs.R

@@ -1,15 +1,15 @@
 tar_test("create tar_resources_qs object", {
-  x <- resources_qs_init(preset = "high")
+  x <- resources_qs_init()
   expect_silent(resources_validate(x))
 })
 
 tar_test("prohibit empty tar_resources_qs object", {
-  x <- resources_qs_init(preset = NULL)
+  x <- resources_qs_init(compress_level = NULL)
   expect_error(resources_validate(x), class = "tar_condition_validate")
 })
 
 tar_test("print tar_resources_qs object", {
-  x <- resources_qs_init(preset = "high")
+  x <- resources_qs_init()
   out <- utils::capture.output(print(x))
   expect_true(any(grepl("tar_resources_qs", out)))
 })

tests/testthat/test-tar_resources_qs.R

@@ -3,14 +3,14 @@ tar_test("tar_resources_qs()", {
   expect_silent(resources_validate(out))
 })
 
-tar_test("tar_resources_qs() default preset", {
+tar_test("tar_resources_qs() non-default compression level", {
   tar_option_set(
     resources = tar_resources(
       qs = tar_resources_qs(
-        preset = "low"
+        compress_level = 4L
       )
     )
   )
   out <- tar_resources_qs()
-  expect_equal(out$preset, "low")
+  expect_equal(out$compress_level, 4L)
 })