Loaded modules

.travis.yml

@@ -32,7 +32,8 @@ r_packages:
 r_github_packages:
  - rstudio/rmarkdown
  - hadley/pkgdown
-
+ - zoonproject/modules@dark_modules
+
 ## After success update the code coverage and deploy the pkgdown to gh-pages
 after_success:
  - Rscript -e 'library(covr);codecov()'

DESCRIPTION

@@ -15,6 +15,8 @@ Description: Reproducible and remixable species distribution modelling. The
     SDM workflows and returns output that is fully reproducible.
 License: BSD_3_clause + file LICENSE
 Imports:
+    remotes,
+    gh,
     dismo,
     methods,
     plyr,

NAMESPACE

@@ -14,10 +14,7 @@ export(FindExtent)
 export(GetMaxEnt)
 export(GetModuleList)
 export(GetPackage)
-export(LoadModule)
 export(Model)
-export(ModuleArguments)
-export(ModuleHelp)
 export(Occurrence)
 export(Output)
 export(Process)
@@ -43,11 +40,11 @@ import(roxygen2)
 import(rworldmap)
 import(sp)
 import(testthat)
-importFrom(RCurl,getURL)
 importFrom(RCurl,url.exists)
 importFrom(SDMTools,auc)
 importFrom(SDMTools,confusion.matrix)
 importFrom(future,future_lapply)
+importFrom(gh,gh)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,grey)
 importFrom(grDevices,png)
@@ -62,8 +59,8 @@ importFrom(stats,na.omit)
 importFrom(utils,browseURL)
 importFrom(utils,capture.output)
 importFrom(utils,data)
-importFrom(utils,download.file)
 importFrom(utils,install.packages)
 importFrom(utils,installed.packages)
 importFrom(utils,methods)
+importFrom(utils,packageDescription)
 importFrom(utils,sessionInfo)

R/sync_modules.R

@@ -0,0 +1,49 @@
+# check the modules are up to date and fetch them if not
+#' @noRd
+#' @importFrom gh gh
+latest_sha <- function() {
+  query <- paste("/repos",
+                 getOption("zoonModulesRepo"),
+                 "branches",
+                 getOption("zoonModulesBranch"),
+                 sep = "/")
+  branch <- gh::gh(query)
+  branch$commit$sha
+}
+
+#' @noRd
+#' @importFrom utils packageDescription
+current_sha <- function () {
+  suppressWarnings(desc <- utils::packageDescription("zoon.modules"))
+  sha <- ""
+  if (inherits(desc, "packageDescription")) {
+    sha <- desc$RemoteSha
+    if (is.null(sha))
+      sha <- ""
+  } 
+  sha
+}
+
+sync_modules <- function () {
+
+  # see if the modules are out of date
+  if (latest_sha() != current_sha()) {
+    message("\nyour zoon modules are out of date")
+
+    # give the user the option to update
+    if (interactive()) {
+
+      message("would you like to update them?")
+      installChoice <- utils::menu(c("yes", "no"))
+
+      if (installChoice == 1) {
+        remotes::install_github(getOption("zoonModulesRepo"), ref = getOption("zoonModulesBranch"),
+                                dependencies = FALSE, quiet = TRUE)
+        message("zoon modules updated")
+      }
+    }
+  }
+
+  # try to load them
+  suppressWarnings(require("zoon.modules", quietly = TRUE))
+}

R/test_outputs.R

@@ -36,15 +36,6 @@ test_occurrence_outputs <- function (roxy_parse, modulePath, en) {
       NaiveRandomRaster <- Crossvalidate <- LogisticRegression <- NULL
       NoProcess <- PrintMap <- NULL
 
-      ## Move these to the sections where they are needed
-      LoadModule("Background")
-      LoadModule("BackgroundAndCrossvalid")
-      LoadModule("Crossvalidate")
-      LoadModule("LogisticRegression")
-      LoadModule("NaiveRandomRaster")
-      LoadModule("NoProcess")
-      LoadModule("PrintMap")
-
       # Load the script
       source(modulePath)
 
@@ -308,13 +299,6 @@ test_covariate_outputs <- function (roxy_parse, modulePath, en) {
         LogisticRegression <- NaiveRandomPresence <- NULL
         PrintMap <- NULL
 
-        ## Move these to the sections where they are needed
-        LoadModule("Background")
-        LoadModule("BackgroundAndCrossvalid")
-        LoadModule("LogisticRegression")
-        LoadModule("NaiveRandomPresence")
-        LoadModule("PrintMap")
-
         # Load the script
         source(modulePath)
 
@@ -455,18 +439,6 @@ test_process_outputs <- function (roxy_parse, modulePath, en) {
       NoProcess <- NULL
       PrintMap <- Domain <- UKAir <- UKAnophelesPlumbeus <- NULL
 
-      ## Move these to the sections where they are needed
-      LoadModule("Background")
-      LoadModule("NaiveRandomPresenceAbsence")
-      LoadModule("Crossvalidate")
-      LoadModule("LogisticRegression")
-      LoadModule("NaiveRandomRaster")
-      LoadModule("NoProcess")
-      LoadModule("PrintMap")
-      LoadModule("Domain")
-      LoadModule("UKAir")
-      LoadModule("UKAnophelesPlumbeus")
-
       # Load the script
       source(modulePath)
 
@@ -780,17 +752,6 @@ test_model_outputs <- function (roxy_parse, modulePath, en) {
       NaiveRandomPresenceAbsence <- NoProcess <- PerformanceMeasures <- NULL
       PrintMap <- UKAir <- UKAnophelesPlumbeus <- NULL
 
-      ## Move these to the sections where they are needed
-      LoadModule("Background")
-      LoadModule("Crossvalidate")
-      LoadModule("NaiveRandomRaster")
-      LoadModule("NaiveRandomPresenceAbsence")
-      LoadModule("NoProcess")
-      LoadModule("PerformanceMeasures")
-      LoadModule("PrintMap")
-      LoadModule("UKAir")
-      LoadModule("UKAnophelesPlumbeus")
-
       # Load the script
       source(modulePath)
 
@@ -1120,12 +1081,6 @@ test_output_outputs <- function (roxy_parse, modulePath, en) {
       Background <- LogisticRegression <- NULL
       UKAir <- UKAnophelesPlumbeus <- NULL
 
-      ## Move these to the sections where they are needed
-      LoadModule("Background")
-      LoadModule("LogisticRegression")
-      LoadModule("UKAir")
-      LoadModule("UKAnophelesPlumbeus")
-
       # Load the script
       source(modulePath)