From 9fd83156be2c0870d3e0fab03111f5e698514bef Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Sun, 18 Apr 2021 11:38:20 +0100
Subject: [PATCH 1/7] Move scales and tictoc to the Imports section

---
 DESCRIPTION | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 29225f5..27e25de 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -51,12 +51,12 @@ Imports:
     MASS,
     parallel,
     progress,
-    progressr
-Suggests:
-    magrittr,
+    progressr,
     scales,
-    testthat,
     tictoc
+Suggests:
+    magrittr,
+    testthat
 Depends: 
     R (>= 3.6)
 Roxygen: list(markdown = TRUE)

From 9daf94d4c71d5f9c89919ab1f8cfcbdfad8e0ca3 Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Sun, 18 Apr 2021 11:42:13 +0100
Subject: [PATCH 2/7] Increment version number

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 27e25de..1958946 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: fxTWAPLS
 Title: An Improved Version of WA-PLS
-Version: 0.0.5
+Version: 0.0.6
 Authors@R: c(
     person(given = "Mengmeng",
            family = "Liu",
diff --git a/NEWS.md b/NEWS.md
index b9221e7..c821a5d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# fxTWAPLS 0.0.6
+
 # fxTWAPLS 0.0.5
 
 * Added support for the `progressr` API (display a progress bar).

From 5660848f1aee0f818d5d6a1df98c5d5aa551fbb9 Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Sun, 18 Apr 2021 12:00:36 +0100
Subject: [PATCH 3/7] Remove LazyData tag

---
 DESCRIPTION | 1 -
 1 file changed, 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1958946..823f1e8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,7 +37,6 @@ Description: The goal of this package is to provide an improved version of
     pseudo-replication.
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
 URL: https://github.com/special-uor/fxTWAPLS/, 
      https://special-uor.github.io/fxTWAPLS/,
      https://research.reading.ac.uk/palaeoclimate/

From 254c2d327dee504aa5dbb567571f34c1a0f2e3c4 Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Fri, 23 Apr 2021 21:03:10 +0100
Subject: [PATCH 4/7] Remove unused tests

---
 tests/testthat.R            |  4 ----
 tests/testthat/test-utils.R | 20 --------------------
 2 files changed, 24 deletions(-)
 delete mode 100644 tests/testthat.R
 delete mode 100644 tests/testthat/test-utils.R

diff --git a/tests/testthat.R b/tests/testthat.R
deleted file mode 100644
index 0a2a303..0000000
--- a/tests/testthat.R
+++ /dev/null
@@ -1,4 +0,0 @@
-library(testthat)
-library(fxTWAPLS)
-
-test_check("fxTWAPLS")
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
deleted file mode 100644
index 5690022..0000000
--- a/tests/testthat/test-utils.R
+++ /dev/null
@@ -1,20 +0,0 @@
-test_that("parallel benchmark works", {
-  # Define toy function that sleeps for (60/cpus) seconds
-  a <- function(cpus) {Sys.sleep(2/cpus)}
-  times_df <- par_benchmark(c(1, 2), a, quiet = TRUE)
-  expect_equal(length(times_df$times), 2)
-  expect_output(par_benchmark(c(2), a, quiet = FALSE))
-  expect_output(par_benchmark(c(2), a, quiet = FALSE, plot = TRUE))
-})
-
-test_that("combine with progress bar works", {
-  # Load binary operator for backend
-  `%do%` <- foreach::`%do%`
-  N <- 5
-  out <- foreach::foreach(i = 1:N, 
-                          .combine = comb_pb(N)) %do% {
-                            Sys.sleep(1)
-                            i
-                          }
-  expect_equal(c(unname(out)), 1:N)
-})
\ No newline at end of file

From 1b72d20b1503f2687e922273e81e14379538deef Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Fri, 23 Apr 2021 21:04:05 +0100
Subject: [PATCH 5/7] Migrate old tests and internal benchmarking functions

---
 R.ignore/tests/testthat.R            |  4 ++
 R.ignore/tests/testthat/test-utils.R | 20 +++++++
 R.ignore/utils-benchmark.R           | 85 +++++++++++++++++++++++++++
 R/utils.R                            | 86 ----------------------------
 4 files changed, 109 insertions(+), 86 deletions(-)
 create mode 100644 R.ignore/tests/testthat.R
 create mode 100644 R.ignore/tests/testthat/test-utils.R
 create mode 100644 R.ignore/utils-benchmark.R

diff --git a/R.ignore/tests/testthat.R b/R.ignore/tests/testthat.R
new file mode 100644
index 0000000..0a2a303
--- /dev/null
+++ b/R.ignore/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(fxTWAPLS)
+
+test_check("fxTWAPLS")
diff --git a/R.ignore/tests/testthat/test-utils.R b/R.ignore/tests/testthat/test-utils.R
new file mode 100644
index 0000000..5690022
--- /dev/null
+++ b/R.ignore/tests/testthat/test-utils.R
@@ -0,0 +1,20 @@
+test_that("parallel benchmark works", {
+  # Define toy function that sleeps for (60/cpus) seconds
+  a <- function(cpus) {Sys.sleep(2/cpus)}
+  times_df <- par_benchmark(c(1, 2), a, quiet = TRUE)
+  expect_equal(length(times_df$times), 2)
+  expect_output(par_benchmark(c(2), a, quiet = FALSE))
+  expect_output(par_benchmark(c(2), a, quiet = FALSE, plot = TRUE))
+})
+
+test_that("combine with progress bar works", {
+  # Load binary operator for backend
+  `%do%` <- foreach::`%do%`
+  N <- 5
+  out <- foreach::foreach(i = 1:N, 
+                          .combine = comb_pb(N)) %do% {
+                            Sys.sleep(1)
+                            i
+                          }
+  expect_equal(c(unname(out)), 1:N)
+})
\ No newline at end of file
diff --git a/R.ignore/utils-benchmark.R b/R.ignore/utils-benchmark.R
new file mode 100644
index 0000000..16e61fd
--- /dev/null
+++ b/R.ignore/utils-benchmark.R
@@ -0,0 +1,85 @@
+#' Perform parallel benchmarks 
+#' 
+#' Perform parallel benchmarks on a function and generate a plot with execution 
+#' times vs CPU count.
+#'
+#' @param CPUS Vector with the number of CPUs.
+#' @param FUN Parallel function, MUST have a parameter called \code{cpus}.
+#' @param plot Boolean flag to request a plot for the results.
+#' @param quiet Boolean flag to print results of each execution.
+#' @param ... Optional arguments for \code{FUN}, must be named; e.g. 
+#'     \code{x = test_df}.
+#'
+#' @examples
+#' # Define toy function that sleeps for (2/cpus) seconds
+#' a <- function(cpus) {Sys.sleep(2/cpus)}
+#' fxTWAPLS:::par_benchmark(c(1, 2), a)
+#' \donttest{
+#' fxTWAPLS:::par_benchmark(c(1, 2), a, plot = TRUE)
+#' }
+#' 
+#' @keywords internal
+#' @noRd
+par_benchmark <- function(CPUS, FUN, plot = FALSE, quiet = FALSE, ...) {
+  cpus <- NULL # Local binding
+  tictoc::tic.clearlog()
+  for (c in CPUS) {
+    tictoc::tic(paste0("Using ", c, " CPUs"))
+    out <- FUN(..., cpus = c)
+    tictoc::toc(log = TRUE, quiet = quiet)
+  }
+  times <- unlist(tictoc::tic.log(format = TRUE))
+  times <- gsub(" sec elapsed", "", unlist(times))
+  times <- gsub(".*: ", "", unlist(times))
+  times <- as.numeric(times)
+  times_df <- data.frame(cpus = CPUS, times = times)
+  
+  if(plot) {
+    print(ggplot2::qplot(cpus, times, data = times_df) + 
+            ggplot2::geom_area(alpha = 0.5) + 
+            ggplot2::geom_line() + 
+            ggplot2::labs(x = "CPUs", y = "Execution time [seconds]") +
+            ggplot2::scale_x_continuous(breaks = 1:max(CPUS)) + 
+            ggplot2::scale_y_continuous(breaks = scales::pretty_breaks(10))
+    )
+  }
+  return(times_df)
+}
+
+#' Combine results with progress bar
+#' 
+#' Combine results with progress bar, to be used in combination with 
+#'     \code{\link[foreach::foreach]{foreach::foreach}}.
+#'     
+#' @importFrom utils flush.console
+#' @importFrom utils setTxtProgressBar
+#' @importFrom utils txtProgressBar
+#' 
+#' @param iterator Number of iterations.
+#' @param FUN Function to combine the results (default: \code{rbind}).
+#' @param ... Optional parameters.
+#' 
+#' @examples
+#' \donttest{
+#' # Load binary operator for backend
+#' `%do%` <- foreach::`%do%`
+#' N <- 5
+#' out <- foreach::foreach(i = 1:N, 
+#'                         .combine = fxTWAPLS:::comb_pb(N)) %do% {
+#'                         Sys.sleep(1)
+#'                         i
+#'                        }
+#' }
+#' 
+#' @noRd
+#' @keywords internal
+comb_pb <- function(iterator, FUN = rbind, ...) {
+  pb <- txtProgressBar(min = 1, max = iterator - 1, style = 3)
+  count <- 0
+  function(...) {
+    count <- count + length(list(...)) - 1
+    setTxtProgressBar(pb, count)
+    flush.console()
+    FUN(...) # this can feed into .combine option of foreach
+  }
+}
\ No newline at end of file
diff --git a/R/utils.R b/R/utils.R
index d137fce..3c0e76b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,89 +1,3 @@
-#' Perform parallel benchmarks 
-#' 
-#' Perform parallel benchmarks on a function and generate a plot with execution 
-#' times vs CPU count.
-#'
-#' @param CPUS Vector with the number of CPUs.
-#' @param FUN Parallel function, MUST have a parameter called \code{cpus}.
-#' @param plot Boolean flag to request a plot for the results.
-#' @param quiet Boolean flag to print results of each execution.
-#' @param ... Optional arguments for \code{FUN}, must be named; e.g. 
-#'     \code{x = test_df}.
-#'
-#' @examples
-#' # Define toy function that sleeps for (2/cpus) seconds
-#' a <- function(cpus) {Sys.sleep(2/cpus)}
-#' fxTWAPLS:::par_benchmark(c(1, 2), a)
-#' \donttest{
-#' fxTWAPLS:::par_benchmark(c(1, 2), a, plot = TRUE)
-#' }
-#' 
-#' @keywords internal
-#' @noRd
-par_benchmark <- function(CPUS, FUN, plot = FALSE, quiet = FALSE, ...) {
-  cpus <- NULL # Local binding
-  tictoc::tic.clearlog()
-  for (c in CPUS) {
-    tictoc::tic(paste0("Using ", c, " CPUs"))
-    out <- FUN(..., cpus = c)
-    tictoc::toc(log = TRUE, quiet = quiet)
-  }
-  times <- unlist(tictoc::tic.log(format = TRUE))
-  times <- gsub(" sec elapsed", "", unlist(times))
-  times <- gsub(".*: ", "", unlist(times))
-  times <- as.numeric(times)
-  times_df <- data.frame(cpus = CPUS, times = times)
-  
-  if(plot) {
-    print(ggplot2::qplot(cpus, times, data = times_df) + 
-            ggplot2::geom_area(alpha = 0.5) + 
-            ggplot2::geom_line() + 
-            ggplot2::labs(x = "CPUs", y = "Execution time [seconds]") +
-            ggplot2::scale_x_continuous(breaks = 1:max(CPUS)) + 
-            ggplot2::scale_y_continuous(breaks = scales::pretty_breaks(10))
-    )
-  }
-  return(times_df)
-}
-
-#' Combine results with progress bar
-#' 
-#' Combine results with progress bar, to be used in combination with 
-#'     \code{\link[foreach::foreach]{foreach::foreach}}.
-#'     
-#' @importFrom utils flush.console
-#' @importFrom utils setTxtProgressBar
-#' @importFrom utils txtProgressBar
-#' 
-#' @param iterator Number of iterations.
-#' @param FUN Function to combine the results (default: \code{rbind}).
-#' @param ... Optional parameters.
-#' 
-#' @examples
-#' \donttest{
-#' # Load binary operator for backend
-#' `%do%` <- foreach::`%do%`
-#' N <- 5
-#' out <- foreach::foreach(i = 1:N, 
-#'                         .combine = fxTWAPLS:::comb_pb(N)) %do% {
-#'                         Sys.sleep(1)
-#'                         i
-#'                        }
-#' }
-#' 
-#' @noRd
-#' @keywords internal
-comb_pb <- function(iterator, FUN = rbind, ...) {
-  pb <- txtProgressBar(min = 1, max = iterator - 1, style = 3)
-  count <- 0
-  function(...) {
-    count <- count + length(list(...)) - 1
-    setTxtProgressBar(pb, count)
-    flush.console()
-    FUN(...) # this can feed into .combine option of foreach
-  }
-}
-
 #' Show progress bar
 #'
 #' @param expr R expression.

From 5f20d055b9f8c81135bc22cc438e7e3cbeb4ab79 Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Fri, 23 Apr 2021 21:04:59 +0100
Subject: [PATCH 6/7] Move the package progress to the list of suggested
 packages, instead of imports (this is used by progressr)

---
 DESCRIPTION | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 823f1e8..e9cc8e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -49,13 +49,12 @@ Imports:
     ggplot2,
     MASS,
     parallel,
+    progressr
+Suggests:
+    magrittr,
     progress,
-    progressr,
     scales,
     tictoc
-Suggests:
-    magrittr,
-    testthat
 Depends: 
     R (>= 3.6)
 Roxygen: list(markdown = TRUE)

From 274870ab3d432c2f6920b0cfe6d775344a4dfabb Mon Sep 17 00:00:00 2001
From: Roberto Villegas-Diaz <villegas.roberto@hotmail.com>
Date: Sat, 24 Apr 2021 18:21:19 +0100
Subject: [PATCH 7/7] Update NEWS

---
 NEWS.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index c821a5d..9bd7147 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,8 @@
 # fxTWAPLS 0.0.6
 
+* Removed unused benchmark functions and test.
+* Simplified the list of suggested packages.
+
 # fxTWAPLS 0.0.5
 
 * Added support for the `progressr` API (display a progress bar).