Merge branch 'development'

.gitignore

@@ -8,6 +8,7 @@ last.dump.rda
 cache/
 figure/
 man/spadesEnv.Rd
+myModule.md
 output/
 tests/testthat/*.pdf
 tests/testthat/*.RData

.travis.yml

@@ -5,32 +5,26 @@
 #   https://github.com/craigcitro/r-travis/wiki
 
 language: r
-
-cran: http://cran.rstudio.com/
-
 sudo: required
+cran: http://cran.rstudio.com/
 
 env:
   global:
     - secure: "KxcKSH4TFMbNMKAj6ePl4yq6SCeYQJcDkw0PMuEdImomwxqY3mP8p+GWVmNN1PKl8k7C/rgLNPAiBoJmddXMzFvGoGRWvyeER0lDN49rzNPHANF9wnMBBYN27mp98hBZlX2Vxu48M3jbmy+wRpmKKvKxTxOa8tUkt0GVEUTPeGQ="
 
 before_install:
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
+  - tlmgr install xcolor
+  - export DISPLAY=:99.0
+  - sh -e /etc/init.d/xvfb start
   - echo "options(repos = c(CRAN='http://cran.rstudio.com'))" >> ~/.Rprofile
-  - "chmod 755 ./_push_vignettes.sh"
+  - chmod 755 ./_push_vignettes.sh
 
 r_build_args: " "
 
 r_check_args: "--as-cran"
 
 warnings_are_errors: true
 
-apt_packages:
-  - curl
-  - latex-xcolor
-  - libcurl4-openssl-dev
-
 r_binary_packages:
   - chron
   - circstats
@@ -69,7 +63,7 @@ r_binary_packages:
 r_github_packages:
   - s-u/fastshp
   - jimhester/covr
-  - rich-iannone/DiagrammeR
+  - MangoTheCat/visualTest
 
 after_success:
   - ./_push_vignettes.sh

DESCRIPTION

@@ -11,8 +11,8 @@ Description: Easily implement a variety of simulation models, with a focus on
     installed with `install.packages("fastshp", repos="http://rforge.net",
     type="source")`.
 URL: https://github.com/PredictiveEcology/SpaDES
-Version: 1.1.0
-Date: 2016-01-25
+Version: 1.1.1
+Date: 2016-02-16
 Authors@R: c(
     person(c("Alex", "M"), "Chubaty", email="[email protected]",
     role=c("aut", "cre")),
@@ -33,16 +33,17 @@ Suggests:
     fastshp,
     knitr,
     Matrix,
+    png,
     RColorBrewer,
     rgdal,
     rmarkdown,
     testthat,
     tkrplot
 Imports:
-    archivist,
+    archivist (>= 2.0),
     CircStats,
     data.table,
-    DiagrammeR,
+    DiagrammeR (>= 0.8.2),
     digest,
     dplyr,
     ff,

NAMESPACE

@@ -57,6 +57,7 @@ export(checkModule)
 export(checkObject)
 export(checkParams)
 export(checkPath)
+export(checkTimeunit)
 export(checkpointFile)
 export(checkpointInterval)
 export(checkpointLoad)
@@ -209,6 +210,7 @@ exportMethods(cache)
 exportMethods(cachePath)
 exportMethods(checkObject)
 exportMethods(checkPath)
+exportMethods(checkTimeunit)
 exportMethods(checkpointFile)
 exportMethods(checkpointInterval)
 exportMethods(clearPlot)
@@ -296,7 +298,7 @@ importFrom(RandomFields,RMexp)
 importFrom(RandomFields,round)
 importFrom(archivist,cache)
 importFrom(archivist,loadFromLocalRepo)
-importFrom(archivist,rmFromRepo)
+importFrom(archivist,rmFromLocalRepo)
 importFrom(archivist,saveToRepo)
 importFrom(archivist,showLocalRepo)
 importFrom(compiler,cmpfun)
@@ -391,6 +393,7 @@ importFrom(raster,extent)
 importFrom(raster,extract)
 importFrom(raster,freq)
 importFrom(raster,getValues)
+importFrom(raster,is.factor)
 importFrom(raster,maxValue)
 importFrom(raster,minValue)
 importFrom(raster,ncell)

NEWS

@@ -1,5 +1,13 @@
 Known issues: https://github.com/PredictiveEcology/SpaDES/issues
 
+version 1.1.1
+=============
+* require `archivist` version 2.0 or greater
+* improved `moduleCoverage` testing  and template (PR257)
+* correct legends from rasters so that `is.factor(raster)` is `TRUE`
+* user defined time units can be used in module metadata "timeunit".
+* add module timeunits to simList show method (#260)
+
 version 1.1.0
 =============
 * require R version 3.2.2 or higher

R/checkpoint.R

@@ -291,24 +291,24 @@ setMethod(
 #' will use the repoDir specified in \code{archivist::setLocalRepo}.
 #'
 #' @export
-#' @importFrom archivist showLocalRepo rmFromRepo
+#' @importFrom archivist showLocalRepo rmFromLocalRepo
 #' @docType methods
 #' @rdname clearStubArtifacts
 #' @author Eliot McIntire
 setGeneric("clearStubArtifacts", function(repoDir = NULL) {
-             standardGeneric("clearStubArtifacts")
-           })
+  standardGeneric("clearStubArtifacts")
+})
 
 #' @export
 #' @rdname clearStubArtifacts
 setMethod(
   "clearStubArtifacts",
   definition = function(repoDir) {
-    md5hashInBackpack = showLocalRepo(repoDir=repoDir)$md5hash
+    md5hashInBackpack = showLocalRepo(repoDir = repoDir)$md5hash
     listFiles <- dir(file.path(repoDir, "gallery")) %>% strsplit(".rda") %>% unlist()
     toRemove <- !(md5hashInBackpack %in% listFiles)
     md5hashInBackpack[toRemove] %>%
-      sapply(., rmFromRepo, repoDir=repoDir)
+      sapply(., rmFromLocalRepo, repoDir = repoDir)
     return(invisible(md5hashInBackpack[toRemove]))
   }
 )

R/environment.R

@@ -32,7 +32,7 @@ setGeneric(".assignSpaDES", function(x, value, ...) {
 setMethod(".assignSpaDES",
           signature(x = "character", value = "ANY"),
           definition = function(x, value, ...) {
-            assign(x, value, envir=.spadesEnv, ...)
+            assign(x, value, envir = .spadesEnv, ...)
 })
 
 #' @rdname assignSpaDES
@@ -199,6 +199,6 @@ setMethod(
   "changeObjEnv",
   signature = c("list", "ANY", "ANY", "ANY"),
   definition = function(x, toEnv, fromEnv, rmSrc) {
-    list2env(x, envir=toEnv)
+    list2env(x, envir = toEnv)
 
 })

R/load.R

@@ -235,7 +235,7 @@ setMethod(
           # The actual load call
           if(identical(loadFun[x], "load")) {
             do.call(getFromNamespace(loadFun[x], loadPackage[x]),
-                                            args = argument, envir=envir(sim))
+                    args = argument, envir = envir(sim))
 
           } else {
             sim[[objectName[x]]] <- do.call(getFromNamespace(loadFun[x], loadPackage[x]),

R/misc-methods.R

@@ -272,10 +272,11 @@ setMethod("normPath",
                   normalizePath(x, winslash = "/", mustWork = FALSE)
                 }
               }) %>%
-              unlist %>%
+              unlist() %>%
               gsub("^[.]", paste0(getwd()), .) %>%
               gsub("\\\\", "//", .) %>%
               gsub("//", "/", .) %>%
+              gsub("^/private/var/", "/var/", .) %>%
               gsub("/$", "", .)
 })
 
@@ -674,3 +675,44 @@ sortDotsFirst <- function(obj) {
   append(obj[dotObjs][order(names(obj[dotObjs]))],
          obj[-dotObjs][order(names(obj[-dotObjs]))])
 }
+
+#' Compare module version against SpaDES package version and warn if incompatible
+#'
+#' Performs a basic check to ensure the module version is compatible with the
+#' SpaDES package version.
+#' Compatibility is best assured when both versions are equal.
+#' If module version < spades version, there is likely no problem, as SpaDES
+#' should be backwards compatible.
+#' However, if module version > spades version, the user needs to update their
+#' version of SpaDES because module compatibility cannot be assured.
+#'
+#' @param moduleName     Character string providing the module name.
+#' @param moduleVersion  The module version as either a character, numeric, or
+#'                       numeric version (e.g., extracted from module metadata).
+#'                       Is coerced to \code{numeric_version}.
+#' @return Logical (invisibly) indicating whether the module is compatible with
+#' the version of the SpaDES package.
+#' Will also produce a warning if not compatible.
+#'
+#' @author Alex Chubaty
+#'
+setGeneric("versionWarning", function(moduleName, moduleVersion) {
+  standardGeneric("versionWarning")
+})
+
+#' @rdname versionWarning
+setMethod(
+  "versionWarning",
+  signature(moduleName = "character", moduleVersion = "ANY"),
+  definition = function(moduleName, moduleVersion) {
+    moduleVersion <- as.numeric_version(moduleVersion)
+    pkgVersion <- packageVersion("SpaDES")
+
+    isOK <- (pkgVersion >= moduleVersion)
+
+    if (!isOK) {
+      warning("Module version (", moduleVersion, ") does not match ",
+              "SpaDES package version (", pkgVersion, ").\n")
+    }
+    return(invisible(isOK))
+})

R/module-repository.R

@@ -1,5 +1,5 @@
 ### deal with spurious httr warnings
-if(getRversion() >= "3.1.0") {
+if (getRversion() >= "3.1.0") {
   utils::globalVariables(c("actualFile", "content", "result"))
 }
 
@@ -161,11 +161,7 @@ setMethod(
     checkModule(name, repo)
     if (is.na(version)) version <- getModuleVersion(name, repo)
 
-    if (packageVersion("SpaDES") != as.numeric_version(version)) {
-      warning("Module version (", as.numeric_version(version),
-              ") does not match SpaDES package version (",
-              packageVersion("SpaDES"), ").\n")
-    }
+    versionWarning(name, version)
 
     zip <- paste0("https://raw.githubusercontent.com/", repo,
                   "/master/modules/", name, "/", name, "_", version, ".zip")
@@ -181,7 +177,7 @@ setMethod(
                             stringsAsFactors = FALSE)
     if (!is.null(children)) {
       if ( all( nzchar(children) & !is.na(children) ) ) {
-        tmp <- lapply(children, function (x) {
+        tmp <- lapply(children, function(x) {
           f <- downloadModule(x, path = path, data = data)
           files2 <<- append(files2, f[[1]])
           dataList2 <<- bind_rows(dataList2, f[[2]])