rm globals(sim) from sampleModules

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PredictiveEcology · Jun 8, 2024 · 40ab4b4 · 40ab4b4
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commit 40ab4b4
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Showing 4 changed files with 13 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,7 +15,7 @@ URL:
     https://spades-core.predictiveecology.org/,
     https://github.com/PredictiveEcology/SpaDES.core
 Date: 2024-06-07
-Version: 2.1.4
+Version: 2.1.5
 Authors@R: c(
     person("Alex M", "Chubaty", , "achubaty@for-cast.ca", role = c("aut"),
            comment = c(ORCID = "0000-0001-7146-8135")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,8 @@
-# SpaDES.core 2.1.3
+# SpaDES.core 2.1.5
 
 * fix issue with Windows short paths in tests;
 * improved documentation;
+* removal of `globals(sim)` in Sample modules
 
 # SpaDES.core 2.1.2
 

diff --git a/inst/sampleModules/fireSpread/fireSpread.R b/inst/sampleModules/fireSpread/fireSpread.R
@@ -30,6 +30,7 @@ defineModule(sim, list(
   reqdPkgs = list("methods", "RColorBrewer", "SpaDES.tools (>= 2.0.0)", "terra"),
   parameters = rbind(
     defineParameter("stackName", "character", "landscape", NA, NA, "name of the RasterStack"),
+    defineParameter("burnStats", "character", "nPixelsBurned", NA, NA, "name of the burn statistics reported"),
     defineParameter("nFires", "numeric", 10L, 1L, 100L, "number of fires to initiate"),
     defineParameter("its", "numeric", 1e6, 1e6, 1e6, "number of iterations for fire spread"),
     defineParameter("persistprob", "numeric", 0.00, 0, 1, "probability of fire persisting in a pixel"),
@@ -51,13 +52,13 @@ defineModule(sim, list(
   inputObjects = bindrows(
     expectsInput(objectName = SpaDES.core::P(sim, module = "fireSpread")$stackName,
                  objectClass = "SpatRaster", desc = NA_character_, sourceURL = NA_character_),
-    expectsInput(objectName = SpaDES.core::globals(sim)$burnStats, objectClass = "numeric",
+    expectsInput(objectName = P(sim)$burnStats, objectClass = "numeric",
                  desc = NA_character_, sourceURL = NA_character_)
   ),
   outputObjects = bindrows(
-    createsOutput(objectName = SpaDES.core::P(sim, module = "fireSpread")$stackName,
+    createsOutput(objectName = P(sim, module = "fireSpread")$stackName,
                   objectClass = "SpatRaster", desc = NA_character_, other = NA_character_),
-    createsOutput(objectName = SpaDES.core::globals(sim)$burnStats, objectClass = "numeric",
+    createsOutput(objectName = P(sim)$burnStats, objectClass = "numeric",
                   desc = NA_character_, other = NA_character_)
   )
 ))
@@ -72,10 +73,10 @@ doEvent.fireSpread <- function(sim, eventTime, eventType, debug = FALSE) {
       ### (use `checkObject` or similar)
       SpaDES.core::checkObject(sim, Par$stackName, layer = "habitatQuality")
 
-      if (is.null(sim[[SpaDES.core::globals(sim)$burnStats]])) {
-        sim[[SpaDES.core::globals(sim)$burnStats]] <- numeric()
+      if (is.null(sim[[P(sim)$burnStats]])) {
+        sim[[P(sim)$burnStats]] <- numeric()
       } else {
-        npix <- sim[[(SpaDES.core::globals(sim)$burnStats)]]
+        npix <- sim[[(P(sim)$burnStats)]]
         stopifnot("numeric" %in% is(npix), "vector" %in% is(npix))
       }
 
@@ -189,11 +190,11 @@ Burn <- function(sim) {
 }
 
 Stats <- function(sim) {
-  npix <- sim[[SpaDES.core::globals(sim)$burnStats]]
+  npix <- sim[[P(sim)$burnStats]]
 
   landscapes <- sim[[Par$stackName]]
 
-  sim[[SpaDES.core::globals(sim)$burnStats]] <- c(npix, length(which(values(landscapes$Fires) > 0)))
+  sim[[P(sim)$burnStats]] <- c(npix, length(which(values(landscapes$Fires) > 0)))
 
   return(invisible(sim))
 }
diff --git a/tests/testthat/test-simulation.R b/tests/testthat/test-simulation.R
@@ -6,7 +6,7 @@ test_that("simulation runs with simInit and spades with set.seed; events arg", {
 
   times <- list(start = 0.0, end = 1, timeunit = "year")
   params <- list(
-    .globals = list(burnStats = "npixelsburned", stackName = "landscape"),
+  #   .globals = list(burnStats = "npixelsburned", stackName = "landscape"),
     randomLandscapes = list(.plotInitialTime = NA, .plotInterval = NA, .seed = list("init" = 321)),
     caribouMovement = list(.plotInitialTime = NA, .plotInterval = NA, torus = TRUE),
     fireSpread = list(.plotInitialTime = NA, .plotInterval = NA)