Merge branch 'fix_fmt_check_runner' into 'master'

Fix fmt check runner

See merge request lpjml/lpjmlkit!92

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2613204'
+ValidationKey: '2634331'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 1.3.2
-date-released: '2024-03-15'
+version: 1.3.3
+date-released: '2024-03-25'
 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: 1.3.2
+Version: 1.3.3
 Authors@R: c(
     person("Jannes", "Breier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -54,4 +54,4 @@ Suggests:
     sf
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2024-03-15
+Date: 2024-03-25

R/write_config.R

@@ -3,7 +3,8 @@
 #' Requires a \link[tibble]{tibble} (modern \link[base]{data.frame} class) in a
 #' specific format (see details & examples) to write the model configuration
 #' file `"config_*.json"`. Each row in the tibble corresponds to a model run.
-#' The generated `"config_*.json"` is based on a js file (e.g. `"lpjml_*.js"`).
+#' The generated `"config_*.json"` is based on a cjson file
+#' (e.g. `"lpjml_config.cjson"`).
 #'
 #' @param x A tibble in a defined format (see details).
 #'
@@ -26,8 +27,8 @@
 #'   individually. Choose between `"annual"`, `"monthly"` or `"daily"`.
 #'
 #' @param output_format Character string defining the format of the output.
-#'   Defaults to `"raw"`. Further options: `"cdf"` (NetCDF) or `"clm"`
-#'   (file with header).
+#'   Defaults to `NULL` (use default from cjson file). Options: `"raw"`,
+#'  `"cdf"` (NetCDF) or `"clm"` (file with header).
 #'
 #' @param cjson_filename Character string providing the name of the main LPJmL
 #'   configuration file to be parsed. Defaults to `"lpjml_config.cjson"`.
@@ -268,7 +269,7 @@ write_config <- function(x,
                          sim_path = NULL,
                          output_list = c(),
                          output_list_timestep = "annual",
-                         output_format = "raw",
+                         output_format = NULL,
                          cjson_filename = "lpjml_config.cjson",
                          parallel_cores = 4,
                          debug = FALSE,
@@ -622,10 +623,29 @@ mutate_config_output <- function(x, # nolint:cyclocomp_linter.
     for (x_id in seq_len(length(x[["output"]]))) {
 
       # Replace output format in x if defined (e.g. raw, clm, cdf)
-      if (x[["output"]][[x_id]]$file$fmt != "txt") {
+      if (!is.null(output_format) &&
+            (is.null(x[["output"]][[x_id]]$file$fmt) ||
+               x[["output"]][[x_id]]$file$fmt != "txt")) {
         x[["output"]][[x_id]]$file$fmt <- output_format
       }
 
+      # make it backwards compatible for old way of explicitly mentioning the
+      #   file extension in the output file name
+      if (!is.null(output_format) && is.null(x[["default_fmt"]])) {
+        new_ext  <- switch(
+          output_format,
+          raw = ".bin",
+          clm = ".clm",
+          cdf = ".nc4"
+        )
+        # Replace file extension of file name in output
+        x[["output"]][[x_id]]$file$name <- sub(
+          "\\.[^.]+$",
+          new_ext,
+          x[["output"]][[x_id]]$file$name
+        )
+      }
+
       # Replace output path in x
       x[["output"]][[x_id]]$file$name <- gsub("output/",
                                               opath,
@@ -641,7 +661,7 @@ mutate_config_output <- function(x, # nolint:cyclocomp_linter.
     # Empty output and include grid if not done
     x["output"] <- list(c())
 
-    if (!("grid" %in% output_list) && !("cdf" %in% output_format)) {
+    if (!("grid" %in% output_list)) {
       output_list <- append(output_list, "grid", after = 0)
       output_timestep <- append(output_timestep, NA, after = 0)
 
@@ -666,17 +686,19 @@ mutate_config_output <- function(x, # nolint:cyclocomp_linter.
         new_output[["id"]] <- output_list[id_ov]
         new_output[["file"]] <- list()
 
-        # Output format three possibilities: netcdf: cdf, raw: bin and clm
-        new_output[["file"]][["fmt"]] <- ifelse(
-          length(output_format) == 1 && is.character(output_format),
-          ifelse(output_list[id_ov] == "globalflux", "txt", output_format),
-          stop(
-            "No valid output_format. Please choose in from \"raw\"",
-            " \"clm\" or \"cdf\" in form of a single character ",
-            "string."
-          )
-        )
 
+        if (!is.null(output_format)) {
+          # Output format three possibilities: netcdf: cdf, raw: bin and clm
+          new_output[["file"]][["fmt"]] <- ifelse(
+            length(output_format) == 1 && is.character(output_format),
+            ifelse(output_list[id_ov] == "globalflux", "txt", output_format),
+            stop(
+              "No valid output_format. Please choose in from \"raw\"",
+              " \"clm\" or \"cdf\" in form of a single character ",
+              "string."
+            )
+          )
+        }
         # Output_timestep could be supplied as a single character string
         #   prescribing a timestep for all outputs or as a character vector
         #   with the length of output_list to assign an individual timestep for
@@ -738,17 +760,26 @@ mutate_config_output <- function(x, # nolint:cyclocomp_linter.
 
         # Create file name with correct path, corresponding outputvar name and
         #   file extension based on the output_format
-        new_output[["file"]][["name"]] <- paste0(
-          opath,
-          output_list[id_ov], ".",
-          ifelse(output_list[id_ov] == "globalflux",
-            "txt",
-            switch(output_format,
-                   raw = "bin",
-                   clm = "clm",
-                   cdf = "nc4")
+        # make it backwards compatible for old way of explicitly mentioning the
+        #   file extension in the output file name
+        if (!is.null(output_format) && is.null(x[["default_fmt"]])) {
+          new_output[["file"]][["name"]] <- paste0(
+            opath,
+            output_list[id_ov], ".",
+            ifelse(output_list[id_ov] == "globalflux",
+              "txt",
+              switch(output_format,
+                     raw = "bin",
+                     clm = "clm",
+                     cdf = "nc4")
+            )
           )
-        )
+        } else {
+          new_output[["file"]][["name"]] <- paste0(
+            opath,
+            output_list[id_ov]
+          )
+        }
 
         # Append new output to output in config
         x[["output"]] <- append(x[["output"]], list(new_output))

README.md

@@ -1,6 +1,6 @@
 # Toolkit for Basic LPJmL Handling <a href=''><img src='inst/img/logo.png' align='right' height='139' /></a>
 
-R package **lpjmlkit**, version **1.3.2**
+R package **lpjmlkit**, version **1.3.3**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lpjmlkit)](https://cran.r-project.org/package=lpjmlkit) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7773134.svg)](https://doi.org/10.5281/zenodo.7773134) [![R build status](https://github.com/PIK-LPJmL/lpjmlkit/workflows/check/badge.svg)](https://github.com/PIK-LPJmL/lpjmlkit/actions) [![codecov](https://codecov.io/gh/PIK-LPJmL/lpjmlkit/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PIK-LPJmL/lpjmlkit) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlkit)](https://pik-piam.r-universe.dev/builds)
 
@@ -76,7 +76,7 @@ In case of questions / problems please contact Jannes Breier <jannesbr@pik-potsd
 
 To cite package **lpjmlkit** in publications use:
 
-Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.3.2, <URL: https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.3.3, <URL: https://github.com/PIK-LPJmL/lpjmlkit>.
 
 A BibTeX entry for LaTeX users is
 
@@ -85,7 +85,7 @@ A BibTeX entry for LaTeX users is
   title = {lpjmlkit: Toolkit for Basic LPJmL Handling},
   author = {Jannes Breier and Sebastian Ostberg and Stephen Björn Wirth and Sara Minoli and Fabian Stenzel and Christoph Müller},
   year = {2024},
-  note = {R package version 1.3.2},
+  note = {R package version 1.3.3},
   doi = {10.5281/zenodo.7773134},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
 }

tests/testthat/test-write_config.R

@@ -351,7 +351,6 @@ test_that("include non output defined outputvars", {
             length(tmp_objects[[1]][["output"]])
           ]]$file$name)
   )
-
 })