Updates to use rewritten reproducible

.github/workflows/R-CMD-check.yaml

@@ -57,7 +57,7 @@ jobs:
         with:
           extra-packages: |
             any::rcmdcheck
-            PredictiveEcology/reproducible@development
+            PredictiveEcology/reproducible@AI
             NLMR=?ignore
           needs: check
 

.github/workflows/pkgdown.yaml

@@ -36,7 +36,7 @@ jobs:
           extra-packages: |
             any::pkgdown
             local::.
-            PredictiveEcology/reproducible@development
+            PredictiveEcology/reproducible@AI
             NLMR=?ignore
           needs: website
 

.github/workflows/revdeps.yaml

@@ -48,7 +48,7 @@ jobs:
         with:
           extra-packages: |
             any::rcmdcheck
-            PredictiveEcology/reproducible@development
+            PredictiveEcology/reproducible@AI
             NLMR=?ignore
           needs: check
 

.github/workflows/test-coverage.yaml

@@ -34,7 +34,7 @@ jobs:
         with:
           extra-packages: |
             any::covr
-            PredictiveEcology/reproducible@development
+            PredictiveEcology/reproducible@AI
             NLMR=?ignore
 
       - name: Install additional package dependencies

.github/workflows/update-citation-cff.yaml

@@ -39,7 +39,7 @@ jobs:
           extra-packages: |
             any::cffr
             any::V8
-            PredictiveEcology/reproducible@development
+            PredictiveEcology/reproducible@AI
             NLMR=?ignore
 
       - name: Install additional package dependencies

DESCRIPTION

@@ -14,8 +14,8 @@ Description: Provides the core framework for a discrete event system to
 URL:
     https://spades-core.predictiveecology.org/,
     https://github.com/PredictiveEcology/SpaDES.core
-Date: 2025-02-25
-Version: 2.1.5.9003
+Date: 2025-04-11
+Version: 2.1.5.9022
 Authors@R: c(
     person("Alex M", "Chubaty", , "achubaty@for-cast.ca", role = c("aut"),
            comment = c(ORCID = "0000-0001-7146-8135")),
@@ -31,7 +31,7 @@ Authors@R: c(
 Depends:
     R (>= 4.3),
     quickPlot (>= 1.0.2),
-    reproducible (>= 2.1.1)
+    reproducible (>= 2.1.2.9027)
 Imports:
     cli,
     data.table (>= 1.11.0),
@@ -40,7 +40,7 @@ Imports:
     lobstr,
     methods,
     qs (>= 0.21.1),
-    Require (>= 0.3.1),
+    Require (>= 1.0.1.9000),
     stats,
     terra (>= 1.7-46),
     tools,
@@ -51,12 +51,15 @@ Suggests:
     CircStats,
     codetools,
     covr,
+    DBI,
     DiagrammeR (>= 0.8.2),
     future,
     future.callr,
     ggplot2,
     ggplotify,
-    httr,
+    gitcreds,
+    googledrive,
+    httr2,
     knitr,
     lattice,
     lme4,
@@ -78,7 +81,8 @@ Suggests:
     withr
 Remotes:
     ropensci/NLMR,
-    PredictiveEcology/reproducible@development
+    PredictiveEcology/reproducible@AI,
+    PredictiveEcology/Require@development
 Additional_repositories: https://predictiveecology.r-universe.dev/
 Encoding: UTF-8
 Language: en-CA
@@ -102,6 +106,7 @@ Collate:
     'code-checking.R'
     'convertToPackage.R'
     'copy.R'
+    'createDESCRIPTIONandDocs.R'
     'debugging.R'
     'downloadData.R'
     'simulation-parseModule.R'

NAMESPACE

@@ -84,6 +84,7 @@ export(conditionalEvents)
 export(convertTimeunit)
 export(convertToPackage)
 export(copyModule)
+export(createDESCRIPTIONandDocs)
 export(createsOutput)
 export(current)
 export(currentModule)
@@ -182,11 +183,13 @@ export(rasterToMemory)
 export(registerOutputs)
 export(remoteFileSize)
 export(reqdPkgs)
+export(restartOrSimInitAndSpades)
 export(restartR)
 export(restartSpades)
 export(rndstr)
 export(saveFiles)
 export(saveSimList)
+export(saveState)
 export(savedSimEnv)
 export(scheduleConditionalEvent)
 export(scheduleEvent)
@@ -397,6 +400,7 @@ importFrom(reproducible,.cacheMessageObjectToRetrieve)
 importFrom(reproducible,.checkCacheRepo)
 importFrom(reproducible,.file.move)
 importFrom(reproducible,.grepSysCalls)
+importFrom(reproducible,.objSizeWithTry)
 importFrom(reproducible,.orderDotsUnderscoreFirst)
 importFrom(reproducible,.preDigestByClass)
 importFrom(reproducible,.prepareOutput)

NEWS.md

@@ -1,8 +1,14 @@
 # SpaDES.core (development version)
 
 * drop support for R 4.2;
+* fix edge case with caching of events; `outputs` would create false positives (i.e., a change, when there wasn't one); this meant that caching would only be successful after the 2nd time running the event, if another module had put objects in the `outputs` list, especially by using `Plots`
 * fix issue with `Plots()` where plots were discarded if no filename was specified;
 * minor documentation improvements;
+* new option: `spades.reqdPkgsDontLoad`, a character vector. If anything is specified, 
+then it will not be loaded with `require` or `library`, but it will be installed, if needed,
+and if `spades.useRequire = TRUE`, which is the default. Default for this new option is
+"box", which is one of potentially many in the R universe that throws an error if it is 
+loaded.
 
 # SpaDES.core 2.1.5
 

R/Plots.R

@@ -147,6 +147,7 @@ ggplotClassesCanHandle <- c("eps", "ps", "tex", "pdf", "jpeg", "tiff", "png", "b
 #'             .plotInitialTime = 1)
 #'     }
 #'   } # end ggplot
+#'   unlink("figures") # clean up
 #' } # end of dontrun
 Plots <- function(data, fn, filename,
                   types = quote(params(sim)[[currentModule(sim)]]$.plots),
@@ -242,7 +243,11 @@ Plots <- function(data, fn, filename,
       if (missing(data)) {
         gg <- fn(...)
       } else {
-        gg <- fn(data, ...)
+        if (is(data, "ggplot")) {
+          gg <- data
+        }
+        else
+          gg <- fn(data, ...)
       }
 
       if (!is(gg, ".quickPlot")) {
@@ -309,18 +314,31 @@ Plots <- function(data, fn, filename,
         names(ggListToScreen) <- gsub(names(ggListToScreen), pattern = " |(\\\n)|[[:punct:]]", replacement = "_")
         Plot(ggListToScreen, addTo = gg$labels$title)
       } else {
-        if (!(identical(fn, plot) || identical(fn, terra::plot)))
+        if ((!(identical(fn, plot) || identical(fn, terra::plot)) || is(gg, "gg")) &&
+            !is(gg, ".quickPlot"))
           print(gg)
       }
     }
   }
   needSaveRaw <- any(grepl("raw", types))
   if (needSave || needSaveRaw) {
     if (missing(filename)) {
-      filename <- tempfile(fileext = "") ## TODO: can we use e.g. the object name + sim time??
+      dataObjName <- deparse(substitute(data))
+      filename <- paste0(dataObjName, "_", basename(gsub("file", "", tempfile(fileext = "")))) ## TODO: can we use e.g. the object name + sim time??
+      if (exists("sim", inherits = FALSE)) {
+        simTime <- round(as.numeric(time(sim)), 3)
+        filename <- paste0("sim", "_", filename)
+      }
     } else {
-      filename <- basename(filename) |> tools::file_path_sans_ext()
+      filename <- filename |> tools::file_path_sans_ext()
+    }
+
+    if (isAbsolutePath(filename)) {
+      path <- dirname(filename)
     }
+
+    filename <- basename(filename)
+
     isDefaultPath <- identical(eval(formals(Plots)$path), path)
     if (!is.null(simIsIn)) {
       if (is(path, "call"))
@@ -333,7 +351,7 @@ Plots <- function(data, fn, filename,
   }
 
   if (needSaveRaw) {
-    if (is(data, "Raster")) {
+    if (is(data, "Raster") || is(data, "SpatRaster")) {
       rasterFilename <- file.path(path, paste0(filename, "_data.tif"))
       writeRaster(data, filename = rasterFilename, overwrite = TRUE)
       if (exists("sim", inherits = FALSE))
@@ -355,7 +373,6 @@ Plots <- function(data, fn, filename,
         )
     }
   }
-
   if (needSave) {
     if (is.null(simIsIn)) {
       if (is.call(path))
@@ -417,7 +434,10 @@ Plots <- function(data, fn, filename,
   if (exists("sim", inherits = FALSE))
     assign("sim", sim, envir = simIsIn)
 
-  return(invisible(NULL))
+  if (exists("gg", inherits = FALSE))
+    return(invisible(gg))
+  else
+    return(invisible(NULL))
 }
 
 #' Test whether there should be any plotting from `.plots` module parameter