Merge pull request #331 from cbeleites/bugfix/321-unit-tests-failing-…

…R-release Clean depracated functions and unit tests
cbeleites · Jul 12, 2021 · a5eee67 · a5eee67
2 parents 63decdc + 922e173
commit a5eee67
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diff --git a/hyperSpec/DESCRIPTION b/hyperSpec/DESCRIPTION
@@ -4,7 +4,7 @@ Type: Package
 Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial,
     Time, Concentration, ...)
 Version: 0.100.0
-Date: 2020-08-24
+Date: 2021-07-10
 Maintainer: Claudia Beleites <[email protected]>
 Authors@R: c(
     person("Claudia",   "Beleites",  role = c("aut", "cre", "dtc"), email = "[email protected]"),
@@ -90,6 +90,7 @@ Collate:
     'DEPRECATED-count_lines.R'
     'hy_options.R'
     'constants-regexps.R'
+    'extract_numbers.R'
     'DEPRECATED-extract_numbers.R'
     'DEPRECATED-ggplot2.R'
     'DEPRECATED-read.ENVI.R'
@@ -113,14 +114,18 @@ Collate:
     'DEPRECATED-scan.R'
     'DEPRECATED-spc-various.R'
     'DEPRECATED-spc_bin.R'
+    'spc_fit_poly.R'
     'DEPRECATED-spc_fit_poly.R'
     'DEPRECATED-spc_fix_colnames.R'
     'DEPRECATED-spc_loess.R'
     'DEPRECATED-spc_na_approx.R'
+    'spc_rubberband.R'
     'DEPRECATED-spc_rubberband.R'
     'DEPRECATED-spc_spline.R'
     'DEPRECATED-wc.R'
     'DEPRECATED-wl_convert_units.R'
+    'normalize01.R'
+    'wl_eval.R'
     'DEPRECATED-wl_eval.R'
     'DEPRECATED-wl_sort.R'
     'DEPRECATED-write_txt_long.R'
@@ -131,7 +136,6 @@ Collate:
     'all.equal.R'
     'apply.R'
     'as.data.frame.R'
-    'extract_numbers.R'
     'as_hyperSpec.R'
     'barbiturates.R'
     'bind.R'
@@ -173,7 +177,6 @@ Collate:
     'merge.R'
     'mergeextra.R'
     'mvtnorm.R'
-    'normalize01.R'
     'palette_colorblind.R'
     'palette_matlab.R'
     'pearson_dist.R'
@@ -193,12 +196,10 @@ Collate:
     'seq.R'
     'show.R'
     'spc_bin.R'
-    'spc_fit_poly.R'
     'spc_fix_colnames.R'
     'spc_identify.R'
     'spc_loess.R'
     'spc_na_approx.R'
-    'spc_rubberband.R'
     'spc_spline.R'
     'split.R'
     'subset.R'
@@ -207,7 +208,6 @@ Collate:
     'vandermonde.R'
     'wl.R'
     'wl_convert_units.R'
-    'wl_eval.R'
     'wl_sort.R'
     'write_txt_long.R'
     'write_txt_wide.R'

diff --git a/hyperSpec/R/DEPRECATED-count_lines.R b/hyperSpec/R/DEPRECATED-count_lines.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-count_lines
 #' @concept moved to hySpc.read.txt
 #'
-#' @title (DEPRECATED) Count Lines (of an ASCII File)
+#' @title (DEPRECATED)
+#'        Count lines (of an ASCII File)
 #'
 #' @description
 #'

diff --git a/hyperSpec/R/DEPRECATED-extract_numbers.R b/hyperSpec/R/DEPRECATED-extract_numbers.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-guess.wavlength
 #' @concept deprecated
 #'
-#' @title (DEPRECATED) Guess Wavelengths from Character Vector
+#' @title (DEPRECATED)
+#'        Guess wavelengths from character vector
 #'
 #'
 #' @description
@@ -16,7 +17,7 @@
 #'
 #' Character vectors used for names (e.g. colnames for matrices or data.frames)
 #' are often treated by [base::make.names()] or similar functions that
-#' produce suitable names (e.g. by prepending "X" to numbers). Such names
+#' produce suitable names (e.g. by pre-pending "X" to numbers). Such names
 #' cannot be directly converted to numeric.
 #'
 #' `guess.wavlength()` tries to extract numbers from X which may be
@@ -35,40 +36,23 @@
 #' tmp <- data.frame(flu[[, , 400 ~ 410]])
 #' (wl <- colnames(tmp))
 #' guess.wavelength(wl)
+#' @include extract_numbers.R
 guess.wavelength <- function(X) {
   # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   hySpc_deprecated("extract_numbers")
   # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-  wl <- regmatches(X, regexpr(.PATTERN.number, X))
-  wl <- as.numeric(wl)
-
-  if (is.null(wl) || length(wl) == 0L || any(is.na(wl))) {
-    if (hy.getOption("debuglevel") >= 1L) {
-      message("could not guess wavelengths")
-    }
-    wl <- NULL
-  }
-
-  wl
+  extract_numbers(X)
 }
 
 #' @include constants-regexps.R
 #' @include hy_options.R
 hySpc.testthat::test(guess.wavelength) <- function() {
   context("guess.wavelength")
 
-  test_that("simple test", {
-    expect_equal(guess.wavelength(1:5), 1:5)
-  })
-
-  test_that("wavelengths containing characters", {
-    wl <- seq(600, 602, length.out = 11)
-    expect_equal(guess.wavelength(make.names(wl)), wl)
-  })
-
-  test_that("return NULL if could not guess wavelenths", {
-    expect_equal(guess.wavelength(colnames(matrix(1:12, 3))), NULL)
-    expect_equal(guess.wavelength(letters[1:4]), NULL)
+  test_that("deprecated", {
+    expect_warning(
+      guess.wavelength(1:5),
+      "Function 'guess.wavelength' is deprecated."
+    )
   })
 }
diff --git a/hyperSpec/R/DEPRECATED-ggplot2.R b/hyperSpec/R/DEPRECATED-ggplot2.R
@@ -2,7 +2,7 @@
 #' @concept moved to hySpc.ggplot2
 #'
 #' @title (DEPRECATED)
-#'        Spectra Plotting with \pkg{ggplot2} Was Moved to \pkg{hySpc.ggplot2}
+#'        Spectra plotting with \pkg{ggplot2} was moved to \pkg{hySpc.ggplot2}
 #'
 #' @description
 #'
@@ -609,3 +609,15 @@ colmix.rgb <- function(x, purecol, against = 1, sub = TRUE,
 
   cols
 }
+
+# Unit tests -----------------------------------------------------------------
+
+hySpc.testthat::test(qplotspc) <- function() {
+  context("ggplot2")
+
+  test_that("deprecated", {
+    expect_warning(res <- qplotspc(flu), "deprecated")
+    expect_warning(res <- qplotmap(flu), "deprecated")
+    expect_warning(res <- qplotc(flu), "deprecated")
+  })
+}
diff --git a/hyperSpec/R/DEPRECATED-read.asc.Andor.R b/hyperSpec/R/DEPRECATED-read.asc.Andor.R
@@ -2,9 +2,9 @@
 #' @concept moved to hySpc.read.txt
 #'
 #' @title (DEPRECATED)
-#'        Import Raman Spectra/Maps from Andor Cameras/Solis ASCII Files
-#' @description
+#'        Import Raman spectra/maps from Andor cameras/solis ASCII files
 #'
+#' @description
 #' These data input functions are **deprecated** and they will be removed in
 #' the next release of \pkg{hyperspec} package.
 #' Now functions in package \pkg{hySpc.read.txt}

diff --git a/hyperSpec/R/DEPRECATED-read.asc.PerkinElmer.R b/hyperSpec/R/DEPRECATED-read.asc.PerkinElmer.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-read.asc.PerkinElmer
 #' @concept moved to hySpc.read.txt
 #'
-#' @title (DEPRECATED) File import filter PerkinElmer ASCII spectra
+#' @title (DEPRECATED)
+#'        File import filter PerkinElmer ASCII spectra
 #'
 #' @description
 #'

diff --git a/hyperSpec/R/DEPRECATED-read.ini.R b/hyperSpec/R/DEPRECATED-read.ini.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-read.ini
 #' @concept moved to hySpc.read.txt
 #'
-#' @title (DEPRECATED) Read INI files
+#' @title (DEPRECATED)
+#'        Read INI files
 #'
 #' @description
 #'

diff --git a/hyperSpec/R/DEPRECATED-read.spe.R b/hyperSpec/R/DEPRECATED-read.spe.R
@@ -158,7 +158,23 @@ read.spe <- function(filename, xaxis = "file", acc2avg = F, cts_sec = F,
   .spc_io_postprocess_optional(spc, filename)
 }
 
-#' Read XML footer from SPE file format version 3.0.
+
+#' @name DEPRECATED-read.spe.xml
+#' @concept moved to hySpc.read.spe
+#'
+#' @title (DEPRECATED)
+#'        Read XML footer from SPE file format version 3.0
+#'
+#' @description
+#'
+#' These data input functions are **deprecated** and they will be removed in
+#' the next release of \pkg{hyperspec} package.
+#' Now functions in package \pkg{hySpc.read.spe}
+#' ([link](https://r-hyperspec.github.io/hySpc.read.spe/reference/index.html))
+#' should be used as the alternatives.
+#'
+#'
+#' **Old description:**
 #'
 #' The new SPE file format, introduced in 2012, was designed to be backwards compatible with the
 #' previous format 2.5. The most prominent change is the new plain text XML footer holding vast
@@ -176,6 +192,10 @@ read.spe <- function(filename, xaxis = "file", acc2avg = F, cts_sec = F,
 #' @importFrom xml2 as_list read_xml
 #'
 .read.spe.xml <- function(filename) {
+  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+  deprecated_read_spe()
+  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
   as_list(read_xml(.read.spe.xml_string(filename)))
 }
 

diff --git a/hyperSpec/R/DEPRECATED-read.txt.Horiba.R b/hyperSpec/R/DEPRECATED-read.txt.Horiba.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-read.txt.Horiba
 #' @concept moved to hySpc.read.txt
 #'
-#' @title (DEPRECATED) Import Horiba Labspec exported ASCII files
+#' @title (DEPRECATED)
+#'        Import Horiba Labspec exported ASCII files
 #'
 #' @description
 #' These data input functions are **deprecated** and they will be removed in

diff --git a/hyperSpec/R/DEPRECATED-read.txt.Renishaw.R b/hyperSpec/R/DEPRECATED-read.txt.Renishaw.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-read.txt.Renishaw
 #' @concept moved to hySpc.read.txt
 #'
-#' @title (DEPRECATED) Import Raman measurements from Renishaw ASCII-files
+#' @title (DEPRECATED)
+#'        Import Raman measurements from Renishaw ASCII-files
 #'
 #' @description
 #'

diff --git a/hyperSpec/R/DEPRECATED-read.txt.Shimadzu.R b/hyperSpec/R/DEPRECATED-read.txt.Shimadzu.R
@@ -1,7 +1,8 @@
 #' @name DEPRECATED-read.txt.Shimadzu
 #' @concept moved to hySpc.read.txt
 #'
-#' @title (DEPRECATED) Reads Shimadzu GCxGC-qMS - Spectra Files (`.txt`)
+#' @title (DEPRECATED)
+#'        Read Shimadzu GCxGC-qMS - spectra files (`.txt`)
 #'
 #' @description
 #'