fix: windows path bug in lcd parser

NEWS.md

@@ -11,6 +11,7 @@
 * Added `...` argument to `read_chroms` for supplying additional arguments to parsers.
 * Added alias to `read_chroms` for reading `mzxml` files with `RaMS`.
 * Added `precision` argument to `call_rainbow` to control number of digits "mz" values are rounded to. (Also changed default behavior so values are rounded to one decimal by default).
+* Fixed bug in `read_shimadzu_lcd` on Windows due to issue with passing escaped paths to Python.
 * Updated documentation of various functions.
 
 ## chromConverter 0.5.0

R/read_shimadzu_lcd.R

@@ -172,7 +172,7 @@ export_stream <- function(path_in, stream, path_out, remove_null_bytes = FALSE,
     reticulate::py_run_string('data = st.read()')
 
     if (missing(path_out)){
-      path_out <- tempfile()
+      path_out <- fs::file_temp()
     }
     if (remove_null_bytes){
       reticulate::py_run_string("data = data.replace(b'\\x00', b'')")

tests/testthat/test-extra.R

@@ -295,27 +295,30 @@ test_that("read_peaklist can read `Shimadzu` ascii (PDA) files", {
   expect_equal(colnames(x[[1]]), c("sample", "rt", "start", "end", "area", "height"))
 })
 
-test_that("read_chroms can read 'Shimadzu' ascii (PDA) files", {
+test_that("read_chroms can read 'Shimadzu' PDA files (ascii and LCD)", {
   skip_on_cran()
   skip_if_not_installed("chromConverterExtraTests")
 
-  path <- system.file("shimadzuDAD_Anthocyanin.txt",
+  path_ascii <- system.file("shimadzuDAD_Anthocyanin.txt",
                       package = "chromConverterExtraTests")
-  skip_if_not(file.exists(path))
+  skip_if_not(file.exists(path_ascii))
 
-  x <- read_chroms(path, format_in = "shimadzu_dad", progress_bar = FALSE)[[1]]
+  path_lcd <- system.file("Anthocyanin.lcd", package = "chromConverterExtraTests")
+  skip_if_not(file.exists(path_lcd))
+
+  x <- read_chroms(path_ascii, format_in = "shimadzu_dad", progress_bar = FALSE)[[1]]
   expect_equal(class(x)[1], "matrix")
   expect_equal(dim(x), c(4689, 328))
   expect_equal(attr(x, "parser"), "chromconverter")
   expect_equal(attr(x, "data_format"), "wide")
 
-  x1 <- read_chroms(path, format_in="shimadzu_dad", progress_bar = FALSE,
+  x1 <- read_chroms(path_ascii, format_in="shimadzu_dad", progress_bar = FALSE,
                     data_format = "long", format_out = "data.frame")[[1]]
   expect_equal(class(x1)[1], "data.frame")
   expect_equal(dim(x1), c(4689*328, 3))
 
-  path <- system.file("Anthocyanin.lcd", package = "chromConverterExtraTests")
-  x2 <- read_chroms(path, progress_bar = FALSE)[[1]]
+
+  x2 <- read_chroms(path_lcd, progress_bar = FALSE)[[1]]
   expect_equal(dim(x2),c(4689,328))
   expect_equal(x, x2, ignore_attr = TRUE)
 })