Change pRojects to allow the use of the checkpoint package (#32)

* Allow checkpoint
* UI improvements

DESCRIPTION

@@ -27,14 +27,20 @@ LazyData: true
 Suggests: 
     covr,
     testthat,
-    knitr,
-    available
+    rmarkdown,
+    xaringan,
+    tufte,
+    revealjs,
+    bookdown
 VignetteBuilder: knitr
 Imports: 
     devtools,
     packrat,
     shiny,
     miniUI,
+    checkpoint,
+    knitr,
+    available,
     methods,
     usethis,
     rmarkdown,

R/createBasicProject.R

@@ -2,7 +2,7 @@
 #'
 #' @param name Project
 #' @param travis Configure Travis-CI
-#' @param packrat Configure Packrat
+#' @param packagedeps Set a tool for package reproducibility
 #' @param git Configure Git
 #' @param readme Include a README
 #'
@@ -17,9 +17,12 @@
 #' }
 createBasicProject <- function(name,
                                travis = TRUE,
-                               packrat = TRUE,
+                               packagedeps = "packrat",
                                git = TRUE,
                                readme = TRUE) {
+
+  packagedeps<-match.arg(packagedeps, c("none","packrat","checkpoint"))
+
   tryCatch({
     if (is_available(name)) {
       dir.create(name)
@@ -35,20 +38,23 @@ createBasicProject <- function(name,
         #placeholder, BADGE stuff
       }
 
-      if (packrat) {
+
+  if (packagedeps == "packrat") {
         desc::desc_set_dep(package = "packrat",
                            type = "Imports",
                            file = usethis::proj_get())
-        packrat::init(file.path(getwd(),
-                                name), enter = FALSE)
-      }
-      if (readme) {
-        usethis::use_readme_rmd(open = FALSE)
-      }
+    packrat::init(name, enter = FALSE)
+  }
 
-      if (git) {
-        usethis::use_git()
-      }
+  if (packagedeps == "checkpoint") {
+        desc::desc_set_dep(package = "checkpoint",
+                           type = "Imports",
+                           file = usethis::proj_get())
+    checkpoint::setSnapshot(Sys.Date(), online = TRUE)
+  }
+
+  if (readme) usethis::use_readme_rmd(open = FALSE)
+  if (git) usethis::use_git()
     }
   }
   ,

R/createTrainingProject.R

@@ -24,11 +24,12 @@ createTrainingProject <- function(name,
   handoutEngine <- match.arg(handoutEngine, c("rmarkdown", "bookdown", "tufte"))
   slideEngine <- match.arg(slideEngine, c("rmarkdown", "revealjs", "xaringan"))
 
-  # Installation dir
-  usePackrat <- !methods::hasArg("packrat")
-  if (!usePackrat)
-    usePackrat <- list(...)[["packrat"]]
-  installDir <- ifelse(usePackrat, name, .libPaths())
+  if(!requireNamespace(handoutEngine, quietly = TRUE)){
+    stop("You need to install ",handoutEngine, " first")
+  }
+  if(!requireNamespace(slideEngine, quietly = TRUE)){
+    stop("You need to install ",slideEngine, " first")
+  }
 
   # Skeleton
   message("Creating skeleton")
@@ -40,7 +41,6 @@ createTrainingProject <- function(name,
     desc::desc_set_dep(package = handoutEngine,
                        type = "Imports",
                        file = usethis::proj_get())
-
     if (handoutEngine != "rmarkdown") {
       message(paste(handoutEngine, "demo added"))
       file.copy(
@@ -71,9 +71,13 @@ createTrainingProject <- function(name,
 
   }
 
-  if (usePackrat) {
-    packrat::snapshot(name)
-    packrat::restore(name)
+  # Perform some basic packrat initialisation
+  if("packagedeps" %in% names(list(...))){
+    pkgdeps <- list(...)[["packagedeps"]]
+    if(pkgdeps == "packrat"){
+      packrat::snapshot(name)
+      packrat::restore(name)
+    }
   }
 
   invisible(TRUE)

R/shinyGadget.R

@@ -20,7 +20,7 @@ projectGadget <- function() {
           shiny::checkboxInput("readme", "Create README", value = TRUE),
           shiny::checkboxInput("git", "Use Git", value = TRUE),
           shiny::checkboxInput("travis", "Use Travis", value = TRUE),
-          shiny::checkboxInput("packrat", "Use Packrat", value = TRUE)
+          shiny::selectInput("packagedeps",label="Use a package for handling reproducibility",choices =  c("none","packrat","checkpoint"), selected = "packrat")
         )
       )
     )
@@ -75,12 +75,12 @@ projectGadget <- function() {
         "Basic"    = createBasicProject(
                         name = input$name, readme = input$readme,
                         git = input$git, travis = input$travis,
-                        packrat = input$packrat),
+                        packagedeps = input$packagedeps),
 
         "Analysis" = createAnalysisProject(
                         name = input$name, dirs = input$dirs,
                         readme = input$readme, git = input$git,
-                        travis = input$travis, packrat = input$packrat),
+                        travis = input$travis, packagedeps = input$packagedeps),
 
         "Package" = createPackageProject(
                         name = input$name, bestPractices = input$bestPractices,
@@ -91,7 +91,7 @@ projectGadget <- function() {
                         handoutEngine = input$handoutE,
                         slideEngine = input$slideE,
                         readme = input$readme, git = input$git,
-                        travis = input$travis, packrat = input$packrat)
+                        travis = input$travis, packagedeps = input$packagedeps)
 
       )
 

inst/rstudio/templates/project/createAnalysisProject.dcf

@@ -20,8 +20,9 @@ Label: Use Git
 Default: On
 Position: right
 
-Parameter: packrat
-Widget: CheckboxInput
-Label: Use Packrat
-Default: On
-Position: right
+Parameter: packagedeps
+Widget: SelectInput
+Label: Reproducibility
+Default: packrat
+Fields: none, packrat, checkpoint
+Position: left

inst/rstudio/templates/project/createBasicProject.dcf

@@ -20,8 +20,9 @@ Label: Use Git
 Default: On
 Position: right
 
-Parameter: packrat
-Widget: CheckboxInput
-Label: Use Packrat
-Default: On
-Position: right
+Parameter: packagedeps
+Widget: SelectInput
+Label: Reproducibility
+Default: packrat
+Fields: none, packrat, checkpoint
+Position: left

inst/rstudio/templates/project/createTrainingProject.dcf

@@ -34,8 +34,9 @@ Label: Use Git
 Default: On
 Position: right
 
-Parameter: packrat
-Widget: CheckboxInput
-Label: Use Packrat
-Default: On
-Position: right
+Parameter: packagedeps
+Widget: SelectInput
+Label: Reproducibility
+Default: packrat
+Fields: none, packrat, checkpoint
+Position: left

tests/testthat/test-createTrainingProject.R

@@ -16,8 +16,7 @@ project_name <- "trainingProject2"
 test_that("createTrainingProject() creates as expected when using defaults",{
 
 
-  proj <- try(createTrainingProject(project_name,
-                                    packrat = FALSE))
+  proj <- try(createTrainingProject(project_name))
 
   if(!inherits(proj, 'try-error')){
     expect_true(file.exists(file.path(project_name, paste0(project_name, ".Rproj"))))
@@ -63,8 +62,7 @@ test_that("createTrainingProject() creates as expected when using tufte and xari
 
   proj <- try(
     createTrainingProject(project_name,
-      handoutEngine = "tufte", slideEngine = "xaringan",
-      packrat = FALSE)
+      handoutEngine = "tufte", slideEngine = "xaringan", packagedeps = "none")
     )
 
   if(!inherits(proj, 'try-error')){

vignettes/BasicProjects.Rmd

@@ -45,13 +45,18 @@ The basic project contains a [`.travis.yml` file](https://docs.travis-ci.com/use
 
 [READ MORE ON TRAVIS-CI](https://docs.travis-ci.com/user/languages/r/)
 
-### Packrat
-[Packrat](https://rstudio.github.io/packrat/) is developed with reproducibility in mind. (Un)fortunately, R moves at an incredible pace and there is the risk that if we're always using the latest versions of packages we can't make our results consistent over time or between users.
+### Reproducibility
+A problem with programming using other people's code is that other people's code changes. This risks your results changing over time. To prevent this, there are some R packages which can help us address this.
 
-Packrat will build a manifest of package versions based on what you use at the point of production. It will then ensure people use the Packrat defined packages, instead of whatever version they have installed.
+[`packrat`](https://rstudio.github.io/packrat/) will build a manifest of package versions based on what you use at the point of production. It will then ensure people use the Packrat defined packages, instead of whatever version they have installed.
 
 [READ MORE ON PACKRAT](https://rstudio.github.io/packrat/)
 
+[`checkpoint`](https://rdrr.io/cran/checkpoint) moves away from using your default CRAN repository and points to a specific repository that has daily snapshots. You then work with CRAN as of a specific date (by default the date you created the project). This is lighter weight than `packrat` but does not help with non-CRAN packages.
+
+
+[READ MORE ON CHECKPOINT](https://rdrr.io/cran/checkpoint)
+
 ### What else?
 We're working on what else should be an optional extra for basic projects and we want your opinions. Contribute your opinion on our [GitHub Issues](https://github.com/lockedata/pRojects/issues).