Merge pull request #286 from PredictiveEcology/Pbug

SpaDES.core::P bugfix; Elapsed time spelling; Elapsed Time units improvement
PredictiveEcology · Jun 7, 2024 · 58a3d19 · 58a3d19
2 parents 45bc4a9 + 16d57dc
commit 58a3d19
Show file tree

Hide file tree

Showing 7 changed files with 21 additions and 17 deletions.
diff --git a/DESCRIPTION b/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: 2024-06-06
-Version: 2.1.3
+Date: 2024-06-07
+Version: 2.1.4
 Authors@R: c(
     person("Alex M", "Chubaty", , "achubaty@for-cast.ca", role = c("aut"),
            comment = c(ORCID = "0000-0001-7146-8135")),

diff --git a/R/restart.R b/R/restart.R
@@ -169,7 +169,8 @@ restartSpades <- function(sim = NULL, module = NULL, numEvents = Inf, restart =
           fd1 <- fd1[!unlist(unname(fd1)) %in% unlist(unname(fd2))]
         }
         # move the changed ones to the simList
-        list2env(objsToCopy[names(fd1)], envir = sim@.xData)
+        if (NROW(fd1))
+          list2env(objsToCopy[names(fd1)], envir = sim@.xData)
       }
 
       modObjNames <- names(sim$.recoverableModObjs[[event]])

diff --git a/R/simList-accessors.R b/R/simList-accessors.R
@@ -525,7 +525,7 @@ P.simList <- function(sim, param, module) {
         modFilePaths <- checkPath(names(mods))
 
         scalls <- sys.calls()
-        whereInSC <- .grepSysCalls(scalls, "^P\\(")
+        whereInSC <- .grepSysCalls(scalls, "^P\\(|^SpaDES.core::P\\(")
         while (whereInSC > 1) {
           poss <- scalls[whereInSC - 1]
           fn <- as.character(poss[[1]][[1]])
@@ -3351,22 +3351,20 @@ elapsedTime.simList <- function(x, byEvent = TRUE, units = "auto", ...) {
     if (identical(units, "auto")) {
       unt <- "secs"
       if (any(a > minutesInSeconds)) {
-        if (any(a > hoursInSeconds)) {
-          if (any(a > daysInSeconds)) {
-            unt <- "days"
-          }
-        } else {
-          unt <- "hours"
-        }
-      } else {
         unt <- "mins"
+      } else if (any(a > hoursInSeconds)) {
+        unt <- "hours"
+      } else if (any(a > daysInSeconds)) {
+        unt <- "days"
       }
-      st <- Sys.time()
-      a <- round(difftime(a + st, st, units = unt), 3) # work around for forcing a non seconds unit, allowing "auto"
     } else {
       # This one won't allow "auto"
+      unt <- units
       units(a) <- units
     }
+    st <- Sys.time()
+    a <- round(difftime(a + st, st, units = unt), 3) # work around for forcing a non seconds unit, allowing "auto"
+
     ret[, elapsedTime := a]
   } else {
     ret <- NULL

diff --git a/R/simulation-simInit.R b/R/simulation-simInit.R
@@ -386,7 +386,7 @@ setMethod(
       sim <- elapsedTimeInSimInit(._startClockTime, sim)
       ._startClockTime <- Sys.time()
       dt <- difftime(._startClockTime, ._startClockTime - sim$._simInitElapsedTime)
-      message("Elpsed time for simInit: ", format(dt, format = "auto"))
+      message("Elapsed time for simInit: ", format(dt, format = "auto"))
     }, add = TRUE)
 
     paths <- lapply(paths, function(p) {

diff --git a/tests/testthat/test-cache.R b/tests/testthat/test-cache.R
@@ -315,7 +315,7 @@ test_that("test .robustDigest for simLists", {
                      "Setting", "Paths", "using dataPath", "Using setDTthreads",
                      "with user supplied tags",
                      "There is no similar item in the cachePath",
-                     "Saving", "Done", "Elpsed time for", sep = "|")
+                     "Saving", "Done", "Elapsed time for", sep = "|")
   expect_true(all(grepl(msgGrep11, mess1)))
 
   msgGrep <- "Running .input|loaded cached copy|module code|Setting|Paths"

diff --git a/tests/testthat/test-mod.R b/tests/testthat/test-mod.R
@@ -75,6 +75,10 @@ test_that("local mod object", {
 
   ## Need "Copy" in this sequence because the event queue is actually an environment :)
   ## so the LHS will have the updated event queue, but the parameters will be at initial conditions
+
+  # quick test for SpaDES.core::P utilization
+  expect_true(SpaDES.core::P(mySim3, "testParB", "test2") == 1197)
+
   expect_true(P(mySim3)$test2$testParB == 1197) # .globals + .inputObjects
   mySim4 <- spades(Copy(mySim3), events = "init")
   expect_true(P(mySim4)$test2$testParB == 1953) ## .globals + .inputObjects + init

diff --git a/tests/testthat/test-simulation.R b/tests/testthat/test-simulation.R
@@ -544,7 +544,7 @@ test_that("conflicting function types", {
                                            "Running .inputObjects|",
                                            "Setting:|Paths set to:|",
                                            "Using setDTthreads|",
-                                           m, ": using dataPath|", "Elpsed")))))
+                                           m, ": using dataPath|", "Elapsed")))))
 
   # assign to sim for functions like scheduleEvent
   lineWithScheduleEvent <- grep(xxx, pattern = "scheduleEvent")[1]
@@ -936,6 +936,7 @@ test_that("simInitAndSpades", {
     spades(debug = FALSE)
 
   expect_true(all.equal(mySim, mySim2))
+
 })
 
 test_that("scheduleEvent with invalid values for eventTime", {