Merge branch 'major_upgrade' into 'master'

major update to version 1.0.0, rearranging code, introducing deprecation to some arguments

See merge request lpjml/lpjmlkit!59

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '1651805'
+ValidationKey: '1943600'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "lpjmlkit: Toolkit for basic LPJmL handling",
-  "version": "0.8.5",
+  "version": "1.0.0",
   "description": "<p>A collection of basic functions to facilitate the work with the\n    Dynamic Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land\n    (LPJmL) hosted at the Potsdam Institute for Climate Impact Research (PIK).\n    It provides functions for performing LPJmL simulations, as well as reading,\n    processing and writing model-related data such as inputs and outputs or\n    configuration files.<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for basic LPJmL handling
-Version: 0.8.5
+Version: 1.0.0
 Authors@R: c(
     person("Jannes", "Breier", , "jannesbr@pik-potsdam.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "ostberg@pik-potsdam.de", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -48,4 +48,4 @@ Suggests:
     maps
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2023-03-17
+Date: 2023-03-20

R/LPJmLData.R

@@ -515,6 +515,3 @@ find_gridfile <- function(searchdir) {
 
   filename
 }
-
-# Avoid note for "."...
-utils::globalVariables(".") # nolint:undesirable_function_linter

R/calc_cellarea.R

@@ -7,11 +7,11 @@
 #' @param x `LPJmLData` object with `$grid` attribute, an LPJmLData object of
 #'   variable `"grid"` (`"LPJGRID"`) or a vector of cell-center latitude
 #'   coordinates in degrees.
-#' @param res_lon Grid resolution in longitude direction in degrees
+#' @param cellsize_lon Grid resolution in longitude direction in degrees
 #'   (default: `0.5`). If `x` is an LPJmLData object the resolution will be
 #'   taken from the meta data included in `x` if available.
-#' @param res_lat Grid resolution in latitude direction in degrees (default:
-#'   same as `res_lon`). If `x` is an LPJmLData object the resolution will be
+#' @param cellsize_lat Grid resolution in latitude direction in degrees (default:
+#'   same as `cellsize_lon`). If `x` is an LPJmLData object the resolution will be
 #'   taken from the meta data included in `x` if available.
 #' @param earth_radius Radius of the sphere (in \eqn{m}) used to calculate the
 #'   cell areas.
@@ -32,8 +32,8 @@
 #'
 #' @export
 calc_cellarea <- function(x, # nolint:cyclocomp_linter.
-                          res_lon = 0.5,
-                          res_lat = res_lon,
+                          cellsize_lon = 0.5,
+                          cellsize_lat = cellsize_lon,
                           earth_radius = 6371000.785,
                           return_unit = "m2"
                          ) {
@@ -58,14 +58,14 @@ calc_cellarea <- function(x, # nolint:cyclocomp_linter.
       stop("Grid attribute is missing. Use method add_grid() to add it.")
     }
 
-    if (!is.null(x$meta$cellsize_lon) && any(res_lon != x$meta$cellsize_lon)) {
-      res_lon <- x$meta$cellsize_lon
-      warning("Using x$meta$cellsize_lon instead of supplied res_lon.")
+    if (!is.null(x$meta$cellsize_lon) && any(cellsize_lon != x$meta$cellsize_lon)) {
+      cellsize_lon <- x$meta$cellsize_lon
+      warning("Using x$meta$cellsize_lon instead of supplied cellsize_lon.")
     }
 
-    if (!is.null(x$meta$cellsize_lat) && any(res_lat != x$meta$cellsize_lat)) {
-      res_lat <- x$meta$cellsize_lat
-      warning("Using x$meta$cellsize_lat instead of supplied res_lat.")
+    if (!is.null(x$meta$cellsize_lat) && any(cellsize_lat != x$meta$cellsize_lat)) {
+      cellsize_lat <- x$meta$cellsize_lat
+      warning("Using x$meta$cellsize_lat instead of supplied cellsize_lat.")
     }
 
     # Check for format of space dimensions, apply different processing
@@ -94,22 +94,22 @@ calc_cellarea <- function(x, # nolint:cyclocomp_linter.
   }
 
   # Check for irregular grid resolution arguments
-  if (length(res_lon) > 1) {
-    warning("res_lon has length ", length(res_lon), ". Using first element.")
-    res_lon <- res_lon[1]
+  if (length(cellsize_lon) > 1) {
+    warning("cellsize_lon has length ", length(cellsize_lon), ". Using first element.")
+    cellsize_lon <- cellsize_lon[1]
   }
-  if (length(res_lon) == 0 || is.na(res_lon)) {
-    stop("Invalid longitude grid resolution 'res_lon'")
+  if (length(cellsize_lon) == 0 || is.na(cellsize_lon)) {
+    stop("Invalid longitude grid resolution 'cellsize_lon'")
   }
-  res_lon <- as.double(res_lon)
-  if (length(res_lat) > 1) {
-    warning("res_lat has length ", length(res_lat), ". Using first element.")
-    res_lat <- res_lat[1]
+  cellsize_lon <- as.double(cellsize_lon)
+  if (length(cellsize_lat) > 1) {
+    warning("cellsize_lat has length ", length(cellsize_lat), ". Using first element.")
+    cellsize_lat <- cellsize_lat[1]
   }
-  if (length(res_lat) == 0 || is.na(res_lat)) {
-    stop("Invalid latitude grid resolution 'res_lat'")
+  if (length(cellsize_lat) == 0 || is.na(cellsize_lat)) {
+    stop("Invalid latitude grid resolution 'cellsize_lat'")
   }
-  res_lat <- as.double(res_lat)
+  cellsize_lat <- as.double(cellsize_lat)
 
   # Check for irregular latitude coordinates
   if (any(x < -90 | x > 90, na.rm = TRUE)) {
@@ -118,7 +118,7 @@ calc_cellarea <- function(x, # nolint:cyclocomp_linter.
 
   cellwidth <- earth_radius * pi / 180
 
-  cellwidth * res_lon * cellwidth * res_lat * cos(x / 180 * pi) %>%
+  cellwidth * cellsize_lon * cellwidth * cellsize_lat * cos(x / 180 * pi) %>%
 
     # Apply conversion factor based on return_unit parameter
     switch(return_unit,

R/check_config.R

@@ -11,8 +11,9 @@
 #' @param model_path Character string providing the path to LPJmL
 #'   (equal to `LPJROOT` environment variable). Defaults to ".".
 #'
-#' @param output_path Character string providing path where an output, a restart
-#'   and a configuration folder are created. If `NULL`, `model_path` is used.
+#' @param sim_path Character string defining path where all simulation data are
+#'   written, including output, restart and configuration files. If `NULL`,
+#'   `model_path` is used. See also [write_config]
 #'
 #' @param return_output Parameter affecting the output. If `FALSE` print
 #'   stdout/stderr message. If `TRUE`, return the result of the check.
@@ -21,6 +22,9 @@
 #' @param raise_error Logical. Whether to raise an error if sub-process has
 #'   non-zero exit status. Defaults to `FALSE`.
 #'
+#' @param output_path Argument is deprecated as of version 1.0; use sim_path
+#'   instead.
+#'
 #' @return NULL.
 #'
 #' @examples
@@ -29,7 +33,7 @@
 #' library(lpjmlkit)
 #'
 #' model_path <- "./LPJmL_internal"
-#' output_path <-"./my_runs"
+#' sim_path <-"./my_runs"
 #'
 #'
 #' # Basic usage
@@ -42,25 +46,30 @@
 #' )
 #'
 #' config_details <- write_config(
-#'   params = my_params,
+#'   x = my_params,
 #'   model_path = model_path,
-#'   output_path = output_path
+#'   sim_path = sim_path
 #' )
 #'
 #' check_config(x = config_details,
 #'   model_path = model_path,
-#'   output_path = output_path,
+#'   sim_path = sim_path,
 #'   return_output = FALSE
 #' )
 #' }
 #' @export
 check_config <- function(x,
                          model_path = ".",
-                         output_path = NULL,
+                         sim_path = NULL,
                          return_output = FALSE,
-                         raise_error = FALSE) {
+                         raise_error = FALSE,
+                         output_path = NULL) {
+
+  sim_path <- deprecate_arg(new_arg = sim_path,
+                            deprec_arg = output_path,
+                            version = "1.0.0")
 
-  if (is.null(output_path)) output_path <- model_path
+  if (is.null(sim_path)) sim_path <- model_path
 
   # Check if x is character (vector). If so convert to tibble for the following.
   if (methods::is(x, "character")) {
@@ -78,7 +87,7 @@ check_config <- function(x,
   config_files <- paste0("config_", x$sim_name, ".json")
 
   if (length(config_files) > 1) {
-      files <- paste0(output_path,
+      files <- paste0(sim_path,
                       "/configurations/",
                       config_files,
                       collapse = " ")
@@ -97,7 +106,7 @@ check_config <- function(x,
   } else {
     inner_command <- paste0(model_path,
                       "/bin/lpjcheck ", # nolint:absolute_path_linter.
-                      output_path,
+                      sim_path,
                       "/configurations/",
                       config_files)
   }
@@ -107,7 +116,8 @@ check_config <- function(x,
   check <- processx::run(command = "sh",
                          args = c("-c", inner_command),
                          error_on_status = raise_error,
-                         cleanup_tree = TRUE)
+                         cleanup_tree = TRUE,
+                         wd = sim_path)
 
   if (!return_output) {
     return(

R/read_io.R

@@ -185,6 +185,7 @@ read_io <- function( # nolint:cyclocomp_linter.
   # Switch off fancy quotes but revert setting when leaving the function
   quotes_option <- options(useFancyQuotes = FALSE) # nolint:undesirable_function_linter.
   on.exit(options(quotes_option)) # nolint:undesirable_function_linter.
+
   # Detect file_type if not provided by user
   if (is.null(file_type)) {
     file_type <- detect_io_type(filename)
@@ -196,6 +197,7 @@ read_io <- function( # nolint:cyclocomp_linter.
       "This function can read files of type ", toString(dQuote(supported_types))
     )
   }
+
   # Check valid dim_order
   valid_dim_names <- c("cell", "time", "band")
   if (!all(dim_order %in% valid_dim_names)) {
@@ -620,7 +622,7 @@ read_io_metadata_meta <- function(filename, file_type, band_names,
     }
   }
   # Prepare additional attributes to be added to metadata
-  additional_attributes <- sapply(
+  additional_attributes <- sapply( # nolint:undesirable_function_linter.
     set_args,
     function(x) unname(get(x)),
     simplify = FALSE
@@ -880,14 +882,3 @@ check_year_subset <- function(subset, meta_data, silent = FALSE) {
   }
   invisible(subset)
 }
-
-# Utility function to replace missing attribute with default value
-default <- function(value, default) {
-  if (is.null(value)) {
-    return(default)
-  } else {
-    return(value)
-  }
-}
-# file_type options supported by read_io
-supported_types <- c("raw", "clm", "meta")