Convert spades.cachePath to reproducible.cachePath

PredictiveEcology · Nov 24, 2018 · 7e82ccf · 7e82ccf
1 parent 8c0d470
commit 7e82ccf
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Showing 11 changed files with 28 additions and 11 deletions.
diff --git a/R/cache.R b/R/cache.R
@@ -295,7 +295,7 @@ setMethod(
         sim <- get("sim", envir = sys.frame(doEventFrameNum))
         cacheRepo <- sim@paths$cachePath
       } else {
-        cacheRepo <- .getOption("spades.cachePath")
+        cacheRepo <- .getOption("reproducible.cachePath")
         #checkPath(cacheRepo, create = TRUE) #SpaDES dependency
       }
     }

diff --git a/R/misc-methods.R b/R/misc-methods.R
@@ -574,7 +574,7 @@ setMethod(
 #' \code{Paths$cachePath} for example instead of \code{getPaths()$cachePath}
 #'
 #' @param cachePath   The default local directory in which to cache simulation outputs.
-#'                    If not specified, defaults to \code{getOption("spades.cachePath")}.
+#'                    If not specified, defaults to \code{getOption("reproducible.cachePath")}.
 #'
 #' @param inputPath   The default local directory in which to look for simulation inputs
 #'                    If not specified, defaults to \code{getOption("spades.inputPath")}.
@@ -613,7 +613,7 @@ setMethod(
 #'
 .paths <- function() {
   list(
-    cachePath = .getOption("spades.cachePath"),
+    cachePath = .getOption("reproducible.cachePath"),
     inputPath = getOption("spades.inputPath"),
     modulePath = getOption("spades.modulePath"),
     outputPath = getOption("spades.outputPath")

diff --git a/R/simList-accessors.R b/R/simList-accessors.R
@@ -1463,7 +1463,7 @@ setReplaceMethod(
 #' If no paths are specified, the defaults are as follows:
 #'
 #' \itemize{
-#'   \item \code{cachePath}: \code{getOption("spades.cachePath")};
+#'   \item \code{cachePath}: \code{getOption("reproducible.cachePath")};
 #'
 #'   \item \code{inputPath}: \code{getOption("spades.modulePath")};
 #'

diff --git a/R/simulation-simInit.R b/R/simulation-simInit.R
@@ -64,7 +64,7 @@ if (getRversion() >= "3.1.0") {
 #' the defaults are as follows:
 #'
 #' \itemize{
-#'   \item \code{cachePath}: \code{getOption("spades.cachePath")};
+#'   \item \code{cachePath}: \code{getOption("reproducible.cachePath")};
 #'
 #'   \item \code{inputPath}: \code{getOption("spades.modulePath")};
 #'

diff --git a/R/spades-core-package.R b/R/spades-core-package.R
@@ -437,7 +437,7 @@
 #'   first time makes the error, the second time has \code{debugonce} and the third time
 #'   is after the error is addressed. \code{TRUE} is likely somewhat slower.
 #'
-#'   \item \code{spades.cachePath}: The default local directory in which to
+#'   \item \code{reproducible.cachePath}: The default local directory in which to
 #'   cache simulation outputs.
 #'   Default is a temporary directory (typically \code{/tmp/RtmpXXX/SpaDES/cache}).
 #'

diff --git a/man/SpaDES.core-package.Rd b/man/SpaDES.core-package.Rd
diff --git a/man/setPaths.Rd b/man/setPaths.Rd
diff --git a/man/simInit.Rd b/man/simInit.Rd
diff --git a/man/simList-accessors-paths.Rd b/man/simList-accessors-paths.Rd
diff --git a/tests/testthat/test-multipleModulePaths.R b/tests/testthat/test-multipleModulePaths.R
@@ -57,7 +57,7 @@ test_that("simulation runs with simInit and spades", {
     init = {
       sim$dp <- dataPath(sim)
       sim$cachePath <- cachePath(sim)
-      sim$optionsCachePath <- getOption("spades.cachePath")
+      sim$optionsCachePath <- getOption("reproducible.cachePath")
       #sim <- scheduleEvent(sim, sim@simtimes$current+1, "test", "event1")
     },
     event1 = {

diff --git a/tests/testthat/test-paths.R b/tests/testthat/test-paths.R
@@ -1,5 +1,6 @@
 test_that("paths file does not work correctly", {
   testInitOut <- testInit(setPaths = FALSE)
+
   on.exit({
     testOnExit(testInitOut)
   }, add = TRUE)
@@ -57,6 +58,20 @@ test_that("paths file does not work correctly", {
                     modulePath = modulePath(mySim),
                     outputPath = outputPath(mySim)), normPath))
 
+  # missing paths
+  oldPaths <- getPaths()
+  do.call(setPaths, paths)
+  on.exit({do.call(setPaths, paths)}, add = TRUE)
+  mySim1 <- simInit(times, params, modules, objects = list())
+  expect_equal(lapply(paths(mySim), normPath),
+               lapply(paths(mySim1), normPath))
+
+  # setting paths via setPaths works for changing the paths in the simInit & therefore simList
+  setPaths(cachePath = oldPaths$cachePath)
+  mySim2 <- simInit(times, params, modules, objects = list())
+  expect_false(identical(lapply(paths(mySim), normPath),
+               lapply(paths(mySim2), normPath)))
+
   inputPath(mySim) <- tmpdir
   expect_equal(inputPath(mySim), tmpdir)
 
@@ -68,4 +83,6 @@ test_that("paths file does not work correctly", {
 
   cachePath(mySim) <- tmpdir
   expect_equal(cachePath(mySim), tmpdir)
+
+
 })