add review recomendations, add test folder

DESCRIPTION

@@ -30,3 +30,6 @@ Imports:
     grDevices,
     maps,
     methods
+
+Suggests:
+    testthat (>= 3.0.0)
\ No newline at end of file

R/average_nyear_window.R

@@ -64,7 +64,7 @@ average_nyear_window <- function(x, # nolint
   interpolate_spline <- function(x, y, nyear_window) {
     rep(NA, dim(y)["year"]) %>%
       `[<-`(seq(round(nyear_window / 2), dim(y)["year"], nyear_window),
-                value = x) %>%
+              value = x) %>%
       zoo::na.spline()
   }
 

R/classify_biomes.R

@@ -62,7 +62,7 @@ classify_biomes <- function(path_reference = NULL,
     stop("files_reference or path_reference must be provided")
   } else if (!is.null(path_reference) && is.null(files_reference)) {
     # Get main file type (meta, clm)
-    file_ext <- get_file_ext(path_reference)
+    file_ext <- get_major_file_ext(path_reference)
 
     # List required output files for each boundary
     output_files <- list_outputs("biome",

R/utils.R

 # function to get file extension
-get_file_ext <- function(path) {
+get_major_file_ext <- function(path) {
   # Get all files in path
   all_files <- list.files(
     path,
@@ -10,12 +10,17 @@ get_file_ext <- function(path) {
   all_file_types <- all_files %>%
     strsplit("/") %>%
     sapply(utils::tail, 1) %>%
-    strsplit("^([^\\.]+)") %>%
+    strsplit("\\.") %>%
     sapply(function(x) {
-      y <- x[2]
-      return(y)
+      y <- x[-1]
+      if ("json" %in% y) {
+        return(paste(tail(strsplit(y, "\\."), 2), collapse = "."))
+      } else {
+        return(tail(strsplit(y, "\\."), 1))
+      }
     }) %>%
-    substr(2, nchar(.))
+    unlist()
+
 
   # Get most frequent file types
   # TODO not yet working
@@ -229,4 +234,4 @@ higher_res <- function(x, y) {
 
 
 # Avoid note for "."...
-utils::globalVariables(".") # nolint:undesirable_function_linter
+utils::globalVariables(".") # nolint:undesirable_function_linter
\ No newline at end of file

tests/testthat.R

+library(testthat)
+library(biospheremetrics)
+
+test_check("biospheremetrics")

tests/testthat/test_detect_io_type.R

+test_that("Detect valid I/O types", {
+  expect_equal(
+    detect_io_type("../testdata/output/pft_npp.bin.json"),
+    "meta"
+  )
+  expect_equal(
+    detect_io_type("../testdata/output/pft_npp.bin"),
+    "raw"
+  )
+  expect_equal(
+    detect_io_type("../testdata/output/pft_npp.clm"),
+    "clm"
+  )
+
+  # Simple text file
+  tmp_filename <- tempfile("lpjmlkit")
+  writeLines("Hello World", tmp_filename)
+  expect_equal(detect_io_type(tmp_filename), "text")
+  file.remove(tmp_filename)
+
+  # Error for non-existing file
+  expect_error(
+    detect_io_type(tmp_filename),
+    "File.*does not exist"
+  )
+})