Merge branch 'multipleModule3' into development

DESCRIPTION

@@ -8,8 +8,8 @@ Description: Provide the core discrete event simulation (DES) framework for
 URL:
     http://spades-core.predictiveecology.org/,
     https://github.com/PredictiveEcology/SpaDES.core
-Date: 2018-11-13
-Version: 0.2.3
+Date: 2018-11-16
+Version: 0.2.3.9000
 Authors@R: c(
     person("Alex M", "Chubaty", email = "alex.chubaty@gmail.com",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7146-8135")),

NEWS.md

@@ -1,13 +1,19 @@
 Known issues: https://github.com/PredictiveEcology/SpaDES.core/issues
 
+version 0.2.4
+=============
+
+## new features
+* An experimental new function and feature, `objectSynonyms`, which will create active bindings of two names to a single object
+* User can now specify `modulePath` as a character vector, e.g., `simInit(..., paths = list(modulePath = c(".", "test")))`. This means that a user can organize the modules in different locations.
+
 version 0.2.3
 =============
 
 ## package dependencies
 * add `RandomFields` to Suggests, as it is in the Suggests of `SpaDES.tools` and used in examples/tests.
 
 ## new features
-* An experimental new function and feature, `objectSynonyms`, which will create active bindings of two names to a single object
 * `simList` internals changed. It now inherits from `environment`. Amongst other things, this means that tab autocomplete in RStudio now works for objects in the `simList`. Also, we removed several associated methods, `$`, `[[`, `ls`, `ls.str`, `objects`, as the defaults for environments work correctly with the `simList` now
 * `debug` arg in `spades` call can now take numeric, currently 1 or 2, giving a few pre-packaged informative messaging each event
 * new function `elapsedTime` which gives a summary of the clock time used by each module or event

R/check.R

@@ -123,12 +123,8 @@ setMethod(
 #'
 #' @param sim    A simList simulation object.
 #'
-#' @param coreModules List of core modules.
-#'
 #' @param coreParams List of default core parameters.
 #'
-#' @param path The location of the modules' source files.
-#'
 #' @param ...    Additional arguments. Not implemented.
 #'
 #' @return  Invisibly return \code{TRUE} indicating object exists; \code{FALSE} if not.
@@ -141,28 +137,31 @@ setMethod(
 #' @author Alex Chubaty
 #'
 # igraph exports %>% from magrittr
-setGeneric("checkParams", function(sim, coreModules, coreParams, path, ...) {
+setGeneric("checkParams", function(sim, coreParams, ...) {
   standardGeneric("checkParams")
 })
 
 #' @rdname checkParams
 setMethod(
   "checkParams",
-  signature(sim = "simList", coreModules = "list", coreParams = "list",
-            path = "character"),
-  definition = function(sim, coreModules, coreParams, path, ...) {
+  signature(sim = "simList", coreParams = "list"),
+  definition = function(sim, coreParams, ...) {
     params <- sim@params
-    modules <- sim@modules
-    userModules <- modules[-which(coreModules %in% modules)]
+    userModules <- modules(sim) # already removes core modules
+    # modules <- sim@modules
+    # userModules <- modules[-which(coreModules %in% modules)]
     globalParams <- sim@params$.globals
     allFound <- TRUE
 
     if (length(userModules)) {
       ### check whether each param in simInit occurs in a module's .R file
       globalsFound <- list()
       readFile <- list()
-      for (uM in userModules) {
-        filename <- paste(path, "/", uM, "/", uM, ".R", sep = "")
+      userModulePaths <- names(userModules)
+
+      for (uMP in userModulePaths) {
+        uM <- basename(uMP)
+        filename <- paste(uMP, "/", uM, ".R", sep = "")
         readFile[[uM]] <- if (!is.null(sim@.xData[[".parsedFiles"]][[filename]])) {
           # a little faster to use already parsed objects --
           #   might have happened earlier during simInit,
@@ -171,8 +170,7 @@ setMethod(
                                   filename = filename)
           deparse(tmp$parsedFile)
         } else {
-          readLines(paste(path, "/", uM, "/", uM, ".R",
-                                            sep = ""))
+          readLines(filename)
         }
 
 

R/misc-methods.R

@@ -135,7 +135,8 @@ setMethod("append_attr",
                 attributes(out[i]) <- attrs[[i]]
               }
             }
-            return(unique(out))
+            dups <- duplicated(out) # unique strips names ... out[!dups] does not
+            return(out[!dups])
 })
 
 ################################################################################
@@ -646,3 +647,12 @@ setPaths <- function(cachePath, inputPath, modulePath, outputPath) {
 
   lapply(.paths(), checkPath, create = TRUE)
 }
+
+.basename <- function (x) {
+  if (is.null(x)) {
+    NULL
+  }
+  else {
+    basename(x)
+  }
+}

R/module-dependencies-methods.R

@@ -116,9 +116,8 @@ setMethod("depsGraph",
             } else {
               el <- depsEdgeList(sim, plot) %>% .depsPruneEdges()
             }
-            core <- .pkgEnv$.coreModules %>% unlist()
-            m <- sim@modules %>% unlist()
-            v <- unique(c(el$to, el$from, m[-which(m %in% core)]))
+            m <- modules(sim) %>% unlist() # modules(sim) doesn't return hidden modules
+            v <- unique(c(el$to, el$from, m)) # so no need to remove them
             return(graph_from_data_frame(el, vertices = v, directed = TRUE))
 })
 

R/simList-accessors.R

@@ -37,7 +37,7 @@ setMethod(
     out[[8]] <- capture.output(cat(">> Modules:\n"))
     ord <- match(unlist(modules(object)), names(timeunits(object))) %>% na.omit
     out[[9]] <- capture.output(print(
-      cbind(Name = modules(object),
+      cbind(Name = unname(modules(object)),
             #Timeunit = c(rep(NA_character_, 4), unname(timeunits(object))[ord])),
             Timeunit = unname(timeunits(object))[ord]),
       quote = FALSE, row.names = FALSE))
@@ -251,7 +251,6 @@ setReplaceMethod(
 #' @param value The object to be stored at the slot.
 #'
 #' @param hidden Logical. If TRUE, show the default core modules.
-#'
 #' @return Returns or sets the value of the slot from the \code{simList} object.
 #'
 #' @family functions to access elements of a \code{simList} object
@@ -2562,16 +2561,23 @@ setMethod(
     } else {
       if (!missing(filenames))  {
         paths <- filenames
-        modules <- sub(basename(paths), replacement = "", pattern = ".R")
+        if (missing(modules)) {
+          modules <- sub(basename(paths), replacement = "", pattern = ".R")
+        }
       } else if (!missing("modules")) {
-        prefix <- if (!missing("paths")) {
-            paths
+        prefix <- if (!file.exists(modules)) {
+          if (!missing("paths")) {
+            pre <- paths
           } else {
-            getOption("spades.modulePath")
+            pre <- getOption("spades.modulePath")
           }
-        paths <- file.path(prefix, modules, paste0(modules, ".R"))
+          file.path(pre, modules)
+        } else {
+          modules
+        }
+        paths <- file.path(prefix, paste0(modules, ".R"))
       } else {
-        stop("one of sim, module, modules, or filename must be supplied.")
+        stop("one of sim, modules, or filename must be supplied.")
       }
 
       if (missing(envir)) {