Move runtime check to tests and other minor changes

.gitignore

@@ -17,6 +17,9 @@
 # ignore libreoffice lock files
 .~*#
 
+# ignore Mac OS files
+.DS_Store
+
 # Ignore everything in "input" folders
 input/
 !input/files

Makefile

@@ -28,6 +28,16 @@ update-renv-all: ## Upgrade all packages (including CRAN packages) in your renv
                  ## to the respective latest release, write renv.lock archive
 	@Rscript -e 'renv::update(); piamenv::archiveRenv()'
 
+upgrade-renv-version: ## Upgrade the renv version and remove
+	@Rscript -e 'renv::upgrade()'
+	@if grep -qE 'attr\(version, *"md5"\) *<- *"[^"]*"' renv/activate.R; then \
+		sed -i -E 's/attr\(version, *"md5"\) *<- *"[^"]*"/attr(version, "md5") <- NULL/' renv/activate.R; \
+		echo "Successfully removed hash from renv/activate.R"; \
+	else \
+		echo "Error: Target pattern 'attr(version, \"md5\") <- \"...\"' not found in renv/activate.R" >&2; \
+		exit 1; \
+	fi
+
 revert-dev-packages: ## All PIK-PIAM packages that are development versions, i.e.
                      ## that have a non-zero fourth version number component, are
                      ## reverted to the highest version lower than the

renv/activate.R

@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.3.0"
+  version <- "1.3.1"
   attr(version, "md5") <- NULL
   attr(version, "sha") <- NULL
 

scripts/start/prepare.R

@@ -5,27 +5,6 @@
 # |  REMIND License Exception, version 1.0 (see LICENSE file).
 # |  Contact: remind@pik-potsdam.de
 
-library(stringr)
-library(glue)
-
-#' check if delimiters only occur paired in a file. No nesting allowed.
-#'
-#' @param file_path where to check
-#' @param openDelim string of the open delimiter
-#' @param closeDelim string of the closing delimiter
-#'
-#' @return boolean
-validatePairedDelimiters <- function(file_path, openDelim = "$onDelim", closeDelim = "$offDelim") {
-  content <- paste(readLines(file_path, warn = FALSE), collapse = "\n")
-  matches <- str_extract_all(content, glue("{str_escape(openDelim)}|{str_escape(closeDelim)}"))[[1]]
-
-  # Build expected alternating sequence
-  expected <- rep_len(c(openDelim, closeDelim), length(matches))
-
-  # Valid if matches alternating pattern AND count is even
-  return(length(matches) %% 2 == 0 && identical(matches, expected))
-}
-
 prepare <- function() {
 
   timePrepareStart <- Sys.time()
@@ -251,10 +230,6 @@ prepare <- function() {
   # $offlisting appears in main.gms but the current process does not let it survive into full.gms
   # therefore all cs3r/cs4r file contents are dumped directly into the full.lst
   # to avoid this we add $offlisting manually at $onDelim present at each include of a cs4r/cs3r
-  # first do a sanity check on "$onDelim", "$offDelim"
-  if (!validatePairedDelimiters(dumpFilePath, "$onDelim", "$offDelim")) {
-    stop("We either have nested $onDelim/$offDelim blocks (unnecessarily large) or $onDelim/$offDelim are not correctly matched.")
-  }
   lucode2::manipulateFile(dumpFilePath, list(c("$onDelim", "$offlisting\n$onDelim"), c("$offDelim", "$offDelim\n$onlisting")), fixed = TRUE)
 
   file.rename(from[exist], to[exist])

tests/testthat/test_03-quick.R

@@ -4,10 +4,36 @@
 # |  AGPL-3.0, you are granted additional permissions described in the
 # |  REMIND License Exception, version 1.0 (see LICENSE file).
 # |  Contact: remind@pik-potsdam.de
+
+library(stringr)
+library(glue)
+
+#' check if delimiters only occur paired in a file. No nesting allowed.
+#'
+#' @param file_path where to check
+#' @param openDelim string of the open delimiter
+#' @param closeDelim string of the closing delimiter
+#'
+#' @return boolean
+validatePairedDelimiters <- function(file_path, openDelim = "$onDelim", closeDelim = "$offDelim") {
+  content <- paste(readLines(file_path, warn = FALSE), collapse = "\n")
+  matches <- str_extract_all(content, glue("{str_escape(openDelim)}|{str_escape(closeDelim)}"))[[1]]
+
+  # Build expected alternating sequence
+  expected <- rep_len(c(openDelim, closeDelim), length(matches))
+
+  # Valid if matches alternating pattern AND count is even
+  return(length(matches) %% 2 == 0 && identical(matches, expected))
+}
+
 test_that("start.R config/tests/scenario_config_quick.csv works", {
   skipIfPreviousFailed()
   output <- localSystem2("Rscript", c("start.R", "config/tests/scenario_config_quick.csv"))
   printIfFailed(output)
   expectSuccessStatus(output)
   expect_true(file.exists("../../output/testOneRegi/REMIND_generic_testOneRegi.mif"))
+
+  # Check if we have nested $onDelim/$offDelim blocks (unnecessarily large) or $onDelim/$offDelim are not correctly matched.
+  # prepare.R contains some string manipulation that might break if this does not hold
+  expect_true(validatePairedDelimiters("../../output/testOneRegi/full.gms", "$onDelim", "$offDelim"))
 })

tutorials/01_GettingREMIND.md

@@ -11,7 +11,7 @@ REQUIREMENTS
 - input data
 - git
 - GAMS >= 39.1.0 with CONOPT license
-- R >= 4.0. We recommend R 4.3.2.
+- R >= 4.0. We recommend R 4.6.1.
 - Windows only: RTools
 - LaTeX
 - pandoc

tutorials/02a_RunningREMINDLocally.md

@@ -9,7 +9,7 @@ Check the general system requirements in [Section 1: Getting REMIND](01_GettingR
 
 - Installed python version must be `< 3.11`. We recommend a python version `3.10.X` as it is closest to being up-to-date while remaining REMIND compatible. To check your python version run `python --version` in a terminal of your choice
 - There are some additional recommendations for running REMIND locally on a **Windows systems**:  
-  - To avoid lengthy compilation times during preparation for your remind run, we recommend to use a version of R for which most R-packages that REMIND depends on, are available as binary packages. This is typically the case for recent versions of R, currently `4.2.X` or `4.3.X`. To check your R version run `R --version` in a terminal of your choice
+  - To avoid lengthy compilation times during preparation for your remind run, we recommend to use a version of R for which most R-packages that REMIND depends on, are available as binary packages. This is typically the case for recent versions of R, currently `4.6.X`. To check your R version run `R --version` in a terminal of your choice
   - As mentioned in the general system requirements, GAMS must be installed. On Windows, make sure that the path to GAMS applications is in your PATH environment variable
   - We recommend to use PowerShell rather than the standard command prompt