move data/ into _episodes/ and _episodes_rmd/

`generate_md_episodes()` is modified such that datasets storred into
_episodes_rmd/data/ needed to knit the episodes, are copied into
_episodes/data/, and are made available at the root of the site.

Author: fmichonneau

data/.gitkeep _episodes/data/.gitkeep

@@ -1,15 +1,41 @@
-if (require("knitr")) {
-    if (packageVersion("knitr") < '1.9.19') {
-        stop("knitr must be version 1.9.20 or higher")
-    }
-} else stop("knitr 1.9.20 or above is needed to build the lessons.")
+generate_md_episodes <- function() {
 
-if (!require("stringr"))
-    stop("The package stringr is required for generating the lessons.")
+    if (require("knitr")) {
+        if (packageVersion("knitr") < '1.9.19') {
+            stop("knitr must be version 1.9.20 or higher")
+        }
+    } else stop("knitr 1.9.20 or above is needed to build the lessons.")
 
-src_rmd <- list.files(pattern = "??-*.Rmd$", path = "_episodes_rmd", full.names = TRUE)
-dest_md <- file.path("_episodes", gsub("Rmd$", "md", basename(src_rmd)))
+    if (!require("stringr"))
+        stop("The package stringr is required for generating the lessons.")
 
-mapply(function(x, y) {
+    ## where the Rmd files and the datasets are located
+    rmd_path <- "_episodes_rmd"
+    rmd_data <- file.path(rmd_path, "data")
+
+    ## where the markdown files and the datasets will end up
+    dest_path <- "_episodes"
+    dest_data <- file.path(dest_path, "data")
+
+    ## find all the Rmd files, and generates the paths for their respective outputs
+    src_rmd <- list.files(pattern = "??-*.Rmd$", path = rmd_path, full.names = TRUE)
+    dest_md <- file.path(dest_path, gsub("Rmd$", "md", basename(src_rmd)))
+
+    ## knit the Rmd into markdown
+    mapply(function(x, y) {
         knitr::knit(x, output = y)
     }, src_rmd, dest_md)
+
+
+    ## copy the datasets from _episodes_rmd/data to _episodes/data
+    rmd_data_files <- list.files(path = rmd_data, full.names = TRUE)
+    dest_data_files <- file.path(dest_data, basename(rmd_data_files))
+
+    if (!dir.exists(file.path(dest_data)))
+        dir.create(file.path(dest_data))
+
+    apply(cbind(rmd_data_files, dest_data_files), 1,
+          function(x) file.copy(x[1], x[2]))
+}
+
+generate_md_episodes()