Address tzdata breaking changes

NEWS.md

@@ -2,6 +2,10 @@
 
 ## Minor changes
 
+* timezones for converted OceanOptics files are now handled differently internally (@Bisaloo, #64), 
+  to handle changes in upstream tzdata 2024b, which removed for example the CET and EST timezone codes.
+  This may result in some other deprecated timezone codes not being handled correctly.
+  Please report any bugs or discrepancies you may notice in the `datetime` field of metadata.
 * lightr now depends on R >= 4.0.0, following the tidyverse recommendation
 * the future package is now explicitly listed as a dependency, removing an `R CMD check` `NOTE` and thus removing the strain on CRAN reviewers. 
   The future package was already a indirect dependency via the future.apply package.

R/parse_avantes_binary.R

@@ -318,7 +318,7 @@ lr_parse_rfl8 <- function(filename, specnum = 1L) {
                                dark_boxcar, white_boxcar, scope_boxcar)
 
     if (specnum == i) {
-      return(list("data" = data, "metadata" = metadata))
+      return(list(data = data, metadata = metadata))
     }
 
   }

R/parse_avantes_converted.R

@@ -90,7 +90,7 @@ lr_parse_ttt <- function(filename) {
 
   data_final[match(colnames(data), cornames)] <- data
 
-  return(list("data" = data_final, "metadata" = metadata))
+  return(list(data = data_final, metadata = metadata))
 }
 
 #' @rdname lr_parse_ttt

R/parse_oceanoptics_converted.R

@@ -61,13 +61,16 @@ lr_parse_jaz <- function(filename) {
   tz <- ""
 
   if (grepl(oo_savetime_regex, savetime)) {
+    # The value we extract here might not follow the official naming and could
+    # not be recognized by tzdata.
     tz <- trimws(gsub(oo_savetime_regex, "\\2", savetime))
     savetime <- gsub(oo_savetime_regex, "\\1 \\3", savetime)
   }
 
   if (tz == "") {
     tz <- "UTC"
   }
+  tz <- convert_backward_tzdata(tz)
 
   # OceanOptics files use locale-dependent date formats but it looks like they
   # are always using English for this, even when the locale is not set to
@@ -163,7 +166,7 @@ lr_parse_jaz <- function(filename) {
 
   data_final[match(colnames(data), cornames)] <- data
 
-  return(list("data" = data_final, "metadata" = unname(metadata)))
+  return(list(data = data_final, metadata = unname(metadata)))
 }
 
 #' @rdname lr_parse_jaz

R/parse_spc.R

@@ -53,6 +53,6 @@ lr_parse_spc <- function(filename) {
 
   metadata <- rep(NA_character_, 13)
 
-  return(list("data" = as.data.frame(data), "metadata" = metadata))
+  return(list(data = as.data.frame(data), metadata = metadata))
 
 }

R/utils.R

@@ -3,3 +3,18 @@
   ifelse(int32 >= 0, int32, 2^31 - 1 + int32)
 
 }
+
+convert_backward_tzdata <- function(tz) {
+
+  # Convert timezones removed in tzdata 2024b.
+  # This is a subset of what tzdata-backward is providing, based on cases we
+  # could observe in test files. It can be expanded based on user feedback and
+  # new test files.
+  switch(
+    tz,
+    EST = "America/Panama",
+    CET = "Europe/Brussels",
+    tz
+  )
+
+}