From 3ffce6b31649f2c9b147c586c32fe5b8c50ca8a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vilmantas=20G=C4=97g=C5=BEna?= <GegznaV@gmail.com>
Date: Tue, 14 Dec 2021 23:13:08 +0200
Subject: [PATCH 1/4] =?UTF-8?q?Rename=20markpeak=20=E2=86=92=20mark=5Fpeak?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 R/DEPRECATED-read.spe.R | 2 +-
 R/mark_peak.R           | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/DEPRECATED-read.spe.R b/R/DEPRECATED-read.spe.R
index 04b26d60..f96fc796 100644
--- a/R/DEPRECATED-read.spe.R
+++ b/R/DEPRECATED-read.spe.R
@@ -346,7 +346,7 @@ spe.showcalpoints <- function(filename, xaxis = "file", acc2avg = F, cts_sec = F
     return("")
   }
 
-  markpeak(spc, wl_convert_units(
+  mark_peak(spc, wl_convert_units(
     from   = hdr$xCalInputUnit,
     to     = .wl_fix_unit_name(xaxis),
     x      = hdr$xCalValues,
diff --git a/R/mark_peak.R b/R/mark_peak.R
index 6d689d38..b5ac16dd 100644
--- a/R/mark_peak.R
+++ b/R/mark_peak.R
@@ -16,8 +16,8 @@
 #' @export
 #' @examples
 #' plot(faux_cell[7])
-#' markpeak(faux_cell[7], 1662)
-markpeak <- function(spc, xpos, col = "red") {
+#' mark_peak(faux_cell[7], 1662)
+mark_peak <- function(spc, xpos, col = "red") {
   assert_hyperSpec(spc)
   validObject(spc)
 

From 890bf0fcfc4fd38a8a29c9eb8c3311c2c1d6107e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vilmantas=20G=C4=97g=C5=BEna?= <GegznaV@gmail.com>
Date: Tue, 14 Dec 2021 23:13:19 +0200
Subject: [PATCH 2/4] Deprecate markpeak

---
 R/DEPRECATED-markpeak.R | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 R/DEPRECATED-markpeak.R

diff --git a/R/DEPRECATED-markpeak.R b/R/DEPRECATED-markpeak.R
new file mode 100644
index 00000000..c7b3b8be
--- /dev/null
+++ b/R/DEPRECATED-markpeak.R
@@ -0,0 +1,35 @@
+#' @name DEPRECATED-markpeak
+#' @concept deprecated
+#'
+#' @title (DEPRECATED)
+#'        Find an evenly spaced grid for x
+#'
+#' @description
+#' These \pkg{hyperSpec} functions are **deprecated** and not maintained any
+#' more. You should not use these.
+#' Currently they are present due to back-compatibility reasons and will be
+#' removed in the next release of the package.
+#' Please, use the suggested alternative functions instead:
+#'
+#' - [hyperSpec::mark_peak()]
+#'
+#'
+#' @param ... arguments to [hyperSpec::mark_peak()].
+#'
+#' @include mark_peak.R
+#' @export
+markpeak <- function(...) {
+  hySpc_deprecated("mark_peak")
+  mark_peak(...)
+}
+
+
+# Unit tests -----------------------------------------------------------------
+
+hySpc.testthat::test(markpeak) <- function() {
+  context("Deprecated functions")
+
+  test_that("markpeak() is deprecated", {
+    expect_error(expect_warning(markpeak(), "deprecated"))
+  })
+}

From 2a46b58a41e98d1ad74cd064f51cfd85cc5655d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vilmantas=20G=C4=97g=C5=BEna?= <GegznaV@gmail.com>
Date: Tue, 14 Dec 2021 23:13:32 +0200
Subject: [PATCH 3/4] Update DESCRIPTION

#44
---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d56d2d17..d607e015 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -98,6 +98,8 @@ Collate:
     'DEPRECATED-ggplot2.R'
     'DEPRECATED-hy_options.R'
     'DEPRECATED-isample.R'
+    'mark_peak.R'
+    'DEPRECATED-markpeak.R'
     'cov_pooled.R'
     'DEPRECATED-pooled.cov.R'
     'raster.R'
@@ -178,7 +180,6 @@ Collate:
     'levelplot.R'
     'map_identify.R'
     'mark_groups_in_dendrogram.R'
-    'mark_peak.R'
     'mean_sd.R'
     'merge.R'
     'mergeextra.R'

From e7a0d09a9cc6b8d3b58a2f1a7ec443d12e78b459 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vilmantas=20G=C4=97g=C5=BEna?= <GegznaV@gmail.com>
Date: Tue, 14 Dec 2021 23:13:42 +0200
Subject: [PATCH 4/4] Update NEWS.md

#44
---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index f9309f6b..04620056 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -36,6 +36,7 @@
      `hy.getOptions()`       | `hy_get_options()`               |  #21
      `hy.setOptions()`       | `hy_set_options()`               |  #21
      `makeraster()`          | `raster_make()`                  |  #47
+     `markpeak()`            | `mark_peak()`                    |  #44
      `matlab.dark.palette()` | `palette_matlab_dark()`          |  cbeleites/hyperSpec#299, cbeleites/hyperSpec#299, @sangttruong
      `matlab.palette()`      | `palette_matlab()`               |  cbeleites/hyperSpec#208, cbeleites/hyperSpec#299, @sangttruong
      `mergeextra()`          | `merge_data()`                   |  cbeleites/hyperSpec#208, cbeleites/hyperSpec#302