Merge branch 'fix_partial_match_warnings' into 'master'

FIxed partial matching in write_config

See merge request lpjml/lpjmlkit!108

Author: jnnsbrr

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3589192'
+ValidationKey: '3612220'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -35,15 +35,6 @@ jobs:
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-
-      - name: Install python dependencies if applicable
-        run: |
-          [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
-          [ -f requirements.txt ] && pip install -r requirements.txt || true
-
       - name: Run pre-commit checks
         shell: bash
         run: |

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'lpjmlkit: Toolkit for Basic LPJmL Handling'
-version: 1.7.8
-date-released: '2025-03-17'
+version: 1.7.9
+date-released: '2025-04-02'
 abstract: A collection of basic functions to facilitate the work with the Dynamic
   Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at
   the Potsdam Institute for Climate Impact Research (PIK). It provides functions for

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.7.8
+Version: 1.7.9
 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")),
@@ -56,4 +56,4 @@ Suggests:
     R6
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2025-03-17
+Date: 2025-04-02

R/LPJmLData_as.R

@@ -451,7 +451,7 @@ LPJmLData$set(
         multi_layer <- multi_dims[which(multi_dims != "cell")]
 
         tmp_rast <- terra::rast(tmp_rast,
-                                nl = dim(data_subset$data)[multi_layer],
+                                nlyrs = dim(data_subset$data)[multi_layer],
                                 vals = NA)
 
         names(tmp_rast) <- dimnames(data_subset$data)[[multi_layer]]
@@ -590,8 +590,8 @@ create_tmp_raster <- function(data_subset, is_terra = FALSE) {
 
   if (is_terra) {
     tmp_raster <- terra::rast(
-      res = c(data_subset$meta$cellsize_lon,
-              data_subset$meta$cellsize_lat),
+      resolution = c(data_subset$meta$cellsize_lon,
+                     data_subset$meta$cellsize_lat),
       xmin = grid_extent[1, 1],
       xmax = grid_extent[2, 1],
       ymin = grid_extent[1, 2],
@@ -602,8 +602,8 @@ create_tmp_raster <- function(data_subset, is_terra = FALSE) {
 
   } else {
     tmp_raster <- raster::raster(
-      res = c(data_subset$meta$cellsize_lon,
-              data_subset$meta$cellsize_lat),
+      resolution = c(data_subset$meta$cellsize_lon,
+                     data_subset$meta$cellsize_lat),
       xmn = grid_extent[1, 1],
       xmx = grid_extent[2, 1],
       ymn = grid_extent[1, 2],

R/LPJmLGridData.R

@@ -123,7 +123,7 @@ LPJmLGridData <- R6::R6Class( # nolint:object_name_linter
 
       # Update grid meta data
       self$.__set_data__(
-        drop_omit(self$data, omit = "cell")
+        drop_omit(self$data, omit_dim = "cell")
       )
 
       # Update grid meta data

R/get_cellindex.R

@@ -9,12 +9,15 @@
 #' to correct it.
 #'
 #' @param grid_filename A string representing the grid file name.
-#' @param extent A numeric vector (lonmin, lonmax, latmin, latmax) containing the
-#'  longitude and latitude boundaries between which values included in the subset.
-#' @param coordinates A list of two named (lon, lat) numeric vectors representing the coordinates.
-#' @param shape A terra SpatVector object in the WGS 84 coordinate reference system
-#' representing the shape to subset the grid.
-#' @param simplify A logical indicating whether to simplify the output to a vector.
+#' @param extent A numeric vector (lonmin, lonmax, latmin, latmax) containing
+#'   the longitude and latitude boundaries between which values included in the
+#'   subset.
+#' @param coordinates A list of two named (lon, lat) numeric vectors
+#'   representing the coordinates.
+#' @param shape A terra SpatVector object in the WGS 84 coordinate reference
+#'   system representing the shape to subset the grid.
+#' @param simplify A logical indicating whether to simplify the output to a
+#'   vector.
 #'
 #'
 #' @return Either an LPJmLData object containing the grid or a vector subsetted
@@ -25,7 +28,8 @@
 #' \dontrun{
 #' get_cellindex(
 #'   grid_filename = "my_grid.bin.json",
-#'   extent = c(-123.25, -122.75, 49.25, 49.75) # (lonmin, lonmax, latmin, latmax)
+#'   extent = c(-123.25, -122.75, 49.25, 49.75) # (lonmin, lonmax, latmin,
+#'                                                 latmax)
 #' )
 #' get_cellindex(
 #'   grid_filename = "my_grid.bin.json",
@@ -39,7 +43,8 @@
 #'
 #' If an `extent` is provided, the function filters the cells to include only
 #' those within the specified longitude and latitude range. The `extent` should
-#' be a numeric vector of length 4 in the form c(lonmin, lonmax, latmin, latmax).
+#' be a numeric vector of length 4 in the form c(lonmin, lonmax, latmin,
+#'                                               latmax).
 #'
 #' If a list of `coordinates` is provided, the function filters the cells to
 #' include only those that match the specified coordinates. The `coordinates`
@@ -58,7 +63,10 @@
 #' specific error messages for different error conditions. For example, it
 #' checks if the `grid_filename` exists, if the `extent` vector has the correct
 #' length, and if the `coordinates` list contains two vectors of equal length.
-get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shape = NULL, simplify = TRUE) {
+get_cellindex <- function(grid_filename, extent = NULL,
+                          coordinates = NULL,
+                          shape = NULL,
+                          simplify = TRUE) {
   # check if filepath is valid
   check_filepath(grid_filename)
   # check if (only) one of extent or coordinates is provided
@@ -85,7 +93,8 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shap
   lon_range <- range(cells$lon)
   lat_range <- range(cells$lat)
 
-  # Check if extent values are within the longitude and latitude range in the cells
+  # Check if extent values are within the longitude and latitude range in the
+  #   cells
   if (!is.null(extent)) {
     cells$cellindex <- as.numeric(row.names(cells)) + 1
 
@@ -118,7 +127,8 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shap
     }
   }
 
-  # Check if coordinates are within the longitude and latitude range in the cells
+  # Check if coordinates are within the longitude and latitude range in the
+  #   cells
   if (!is.null(coordinates)) {
     out_of_bounds <- coordinates[[1]] < lon_range[1] |
       coordinates[[1]] > lon_range[2] |
@@ -161,7 +171,8 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shap
       dplyr::select("x", "y")
 
     cells <- grid_lonlat |>
-      subset(coordinates = lapply(list(lon = cell_coords$x, lat = cell_coords$y),
+      subset(coordinates = lapply(list(lon = cell_coords$x,
+                                       lat = cell_coords$y),
                                   FUN = as.character))
   }
 
@@ -189,7 +200,8 @@ check_extent <- function(extent) {
     stop("extent must be a numeric vector of length 4.")
   }
 
-  # check if character vector present and convert to numeric (to be consistent with coordinates) # nolint
+  # check if character vector present and convert to numeric (to be consistent
+  #   with coordinates)
   if (is.character(extent)) {
     extent <- as.numeric(extent)
   }
@@ -207,7 +219,8 @@ check_extent <- function(extent) {
 # Check if both extent and coordinates are provided
 check_multiple <- function(extent, coordinates, shape) {
   if (is.null(extent) && is.null(coordinates) && is.null(shape)) {
-    warning("Neither extent, coordinates or shape provided. Full grid will be returned.")
+    warning("Neither extent, coordinates or shape provided.",
+            " Full grid will be returned.")
   }
   if ((!is.null(extent) && !is.null(coordinates)) ||
         (!is.null(extent) && !is.null(shape)) ||
@@ -236,15 +249,17 @@ correct_extent <- function(extent) {
   extent
 }
 
-# Check if the coordinates are a list of two numeric vectors and of equal length
+# Check if the coordinates are a list of two numeric vectors and of equal
+#   length
 check_coordinates <- function(coordinates) {
   if (!is.list(coordinates) || length(coordinates) != 2) {
     stop("coordinates must be a list of two vectors.")
   }
 
   coordinates <- lapply(coordinates, function(coord) {
     if (!is.numeric(coord)) {
-      warning("Non-numeric coordinates detected, attempting to convert to numeric.")
+      warning("Non-numeric coordinates detected,",
+              " attempting to convert to numeric.")
       coord <- as.numeric(coord)
       if (any(is.na(coord))) {
         stop("Unable to convert all coordinates to numeric.")

R/read_config.R

@@ -55,7 +55,7 @@ read_config <- function(filename,
   # Read compiled config files. detect_io_type returns "json" for pure JSON without
   # comments.
   if (tolower(file_type) == "json") {
-    tmp_json <- jsonlite::read_json(path = filename, simplify = FALSE)
+    tmp_json <- jsonlite::read_json(path = filename, simplifyVector = FALSE)
 
   } else {
     # Read compilable cjson or js files - the standard default config files. These

R/read_meta.R

@@ -36,10 +36,10 @@ read_meta <- function(filename, ...) {
 
   # Meta (JSON) file handling
   if (file_type == "meta") {
-    meta_object <- jsonlite::read_json(path = filename, simplify = TRUE) %>%
+    meta_object <- jsonlite::read_json(path = filename, simplifyVector = TRUE) %>%
       LPJmLMetaData$new(data_dir = pathname)
 
-  # Handling of input or output file containing a header
+    # Handling of input or output file containing a header
   } else if (file_type == "clm") {
     header <- read_header(filename, ...)
     additional_attributes <- list(
@@ -53,7 +53,7 @@ read_meta <- function(filename, ...) {
       data_dir = pathname
     )
 
-  # Other formats are not supported yet
+    # Other formats are not supported yet
   } else {
     stop("Non readable (meta) file format.")
   }

R/write_config.R

@@ -598,7 +598,7 @@ parse_config <- function(path,
                             ),
                             wd = path,
                             cleanup_tree = TRUE)$stdout %>%
-    jsonlite::parse_json(simplify = FALSE)
+    jsonlite::parse_json(simplifyVector = FALSE)
 
   tmp_json
 }