Merge branch 'cjson_files_default' into 'master'

add support for new cjson files with new arg to write_config - cjson_filename....

See merge request lpjml/lpjmlkit!85

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2362200'
+ValidationKey: '2560480'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -23,6 +23,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
+            gamstransfer=?ignore
             any::lucode2
             any::covr
             any::madrat
@@ -56,6 +57,8 @@ jobs:
 
       - name: Test coverage
         shell: Rscript {0}
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
+          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
         env:
           NOT_CRAN: "true"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9019
+    rev: v0.3.2.9025
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

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: 1.2.0
-date-released: '2023-11-24'
+version: 1.3.0
+date-released: '2023-12-05'
 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: 1.2.0
+Version: 1.3.0
 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: 2023-11-24
+Date: 2023-12-05

R/read_config.R

@@ -57,12 +57,12 @@ read_config <- function(filename,
   if (tolower(file_type) == "json") {
     tmp_json <- jsonlite::read_json(path = filename, simplify = FALSE)
 
-  # Read compilable cjson or js files - the standard default config files. These
-  # should be detected as "text" by detect_io_type.
   } else {
+    # Read compilable cjson or js files - the standard default config files. These
+    # should be detected as "text" by detect_io_type.
     tmp_json <- parse_config(
       path = dirname(filename),
-      js_filename = basename(filename),
+      cjson_filename = basename(filename),
       from_restart = from_restart,
       macro = macro
     )

R/utils.R

@@ -1,15 +1,18 @@
 # Collection of small utility function applied across the package
 
 # Function to deprecate a function argument that is replaced by a new one
-deprecate_arg <- function(new_arg, deprec_arg, version = "1.0.0") {
+deprecate_arg <- function(new_arg,
+                          deprec_arg,
+                          version = "1.0.0",
+                          ignore_new_arg = FALSE) {
 
   new_name <- deparse(substitute(new_arg))
   deprec_name <- deparse(substitute(deprec_arg))
 
   # Only if deprecated argument is set
   if (!is.null(deprec_arg)) {
 
-    if (is.null(new_arg)) {
+    if (is.null(new_arg) || ignore_new_arg) {
       new_arg <- deprec_arg
 
     } else {