Merge pull request #72 from jhudsl/cansavvy/example-fix

Fixing example file copy over function

NAMESPACE

@@ -43,7 +43,7 @@ export(replace_html)
 export(replace_single_html)
 export(set_knitr_image_path)
 export(simple_references)
+importFrom(fs,dir_copy)
 importFrom(magrittr,"%>%")
 importFrom(readr,write_tsv)
 importFrom(utils,download.file)
-importFrom(utils,unzip)

R/coursera.R

@@ -213,6 +213,7 @@ convert_coursera_quizzes <- function(input_quiz_dir = "quizzes",
 #' @export
 #' @rdname coursera
 #'
+#' @importFrom utils download.file
 #'
 render_coursera <- function(
   output_dir = file.path("docs", "coursera"),

R/example_data.R

@@ -10,6 +10,7 @@
 good_quiz_path <- function() {
   list.files(
     pattern = "quiz_good.md$",
+    recursive = TRUE,
     system.file("extdata", package = "leanbuild"),
     full.names = TRUE
   )
@@ -25,6 +26,7 @@ good_quiz_path <- function() {
 bad_quiz_path <- function() {
   list.files(
     pattern = "quiz_bad.md$",
+    recursive = TRUE,
     system.file("extdata", package = "leanbuild"),
     full.names = TRUE
   )
@@ -35,80 +37,59 @@ bad_quiz_path <- function() {
 #' @param dest_dir The destination directory you would like the example repo files to be placed. By default is current directory.
 #' @export
 #'
-#' @importFrom utils download.file
-#' @importFrom utils unzip
+#' @importFrom fs dir_copy
 #' @examples
+#' # Run this to get the files we need
+#' example_files <- leanbuild::example_repo_setup()
 #'
-#' example_repo_setup()
 example_repo_setup <- function(dest_dir = ".") {
 
-  zip_file <- file.path(dest_dir, "example-repo.zip")
+  bookdown_path <- list.files(
+    pattern = "_bookdown.yml$",
+    system.file("extdata/", package = "leanbuild"),
+    full.names = TRUE
+  )
+
+  # Copy over whole directory
+  fs::dir_copy(dirname(bookdown_path), dest_dir, overwrite = TRUE)
 
-  if (!dir.exists(dest_dir)) {
-    dir.create(dest_dir)
-  }
-  download.file(url = "https://github.com/jhudsl/DaSL_Course_Template_Leanpub/raw/main/example-repo.zip",
-                destfile = zip_file)
+  copied_files <- list.files(dirname(bookdown_path), full.names = TRUE)
 
-  # See what unzip is being used
-  operating_system <- Sys.info()[1]
-  message(operating_system)
-  if (operating_system == "Windows" ){
-    # Unzip function doesn't always work for windows
-    system(paste("7z a -tzip", zip_file, dest_dir))
-  } else {
-    # Unzip the folder
-    utils::unzip(zip_file, exdir = dest_dir)
-  }
+  return(copied_files)
 }
 
 #' Clean up example repo files
 #'
-#' @param dir What directory to delete the example files from
+#' @param files_to_remove List of example files to delete.
+#' @param verbose TRUE/FALSE would you like progress messages?
 #' @export
 #'
 #' @examples
 #'
-#' example_repo_cleanup()
+#' # Run this to get the files we need
+#' example_files <- leanbuild::example_repo_setup()
 #'
-example_repo_cleanup <- function(dir = ".") {
-
-  file_list <- file.path(dir, "resources", "needed_leanbuild_files.txt")
-  if (file.exists(file_list)) {
-    file_list <- readLines(file.path(dir, "resources", "needed_leanbuild_files.txt"))
-  } else {
-    file_list <- NULL
-  }
-  # Find example folder file
-  files_to_remove <- c(
-    file_list,
-    "_bookdown.yml",
-    "_output.yml",
-    "01-intro.Rmd",
-    "02-chapter_of_course.Rmd",
-    "About.Rmd",
-    "assets",
-    "docs",
-    "example-repo.zip",
-    "index.Rmd",
-    "quizzes",
-    "resources",
-    "Course_Name.rds",
-    "manuscript",
-    "question_error_report.tsv",
-    "packages.bib")
-
+#' # Run this to delete them
+#' example_repo_cleanup(files_to_remove = basename(example_files))
+#'
+example_repo_cleanup <- function(files_to_remove, verbose = FALSE) {
 
   message("Cleaning up and removing example repo files")
 
-  # Now remove it all
-  lapply(files_to_remove, function(file) {
-    if (file.exists(file) | dir.exists(file)) {
-      system(paste0("chmod +w -R", file))
-      system(paste0("sudo rm -r ", file))
+  files_to_remove <- c(list.files("quizzes", recursive = TRUE, full.names = TRUE),
+                       list.files("docs", recursive = TRUE, full.names = TRUE),
+                       list.files("manuscript",  recursive = TRUE, full.names = TRUE),
+                       list.files("resources", recursive = TRUE, full.names = TRUE),
+                       files_to_remove,
+                       "question_error_report.tsv",
+                       "Course_Name.rds"
+  )
+
+  lapply(files_to_remove, function(file2remove, verbose = verbose) {
+    if (file.exists(file2remove)) {
+      message(paste0("Removing: ", file2remove))
+      file.remove(file2remove)
     }
   })
-}
 
-# save(bad_quiz, bad_quiz, file = "bad_quiz.RData")
-# save(good_quiz, good_quiz, file = "good_quiz.RData")
+}

inst/extdata/01-intro.Rmd

@@ -0,0 +1,20 @@
+---
+title: "Course Title"
+---
+
+```{r, include = FALSE}
+leanbuild::set_knitr_image_path()
+```
+
+# Introduction
+
+## Motivation
+This course will cover
+
+**Target Audience:**  
+The course is intended for
+
+**Curriculum:**  
+The curriculum will cover
+
+This course was funded by

inst/extdata/02-example-chapter.Rmd

@@ -0,0 +1,111 @@
+---
+title: "Example Chapter"
+---
+
+# Example Chapter
+
+Every chapter needs to start out with this chunk of code:
+
+```{r, include = FALSE}
+leanbuild::set_knitr_image_path()
+```
+
+### Code examples
+
+You can demonstrate code like this:
+
+```{r}
+output_dir <- file.path("resources", "code_output")
+if (!dir.exists(output_dir)) {
+  dir.create(output_dir)
+}
+```
+
+And make plots too:
+
+```{r}
+hist_plot <- hist(iris$Sepal.Length)
+```
+
+You can also save these plots to file:
+
+```{r}
+png(file.path(output_dir, "test_plot.png"))
+hist_plot
+dev.off()
+```
+
+### Image example
+
+
+How to include a Google slide.
+
+```{r, fig.align='center', echo = FALSE, fig.alt= "Major point!! example image"}
+leanbuild::include_slide("https://docs.google.com/presentation/d/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ/edit#slide=id.gcc4fbee202_0_141")
+```
+
+But if you have the slide or some other image locally downloaded you can also use html like this:
+
+<img src="resources/images/02-example-chapter_files/figure-html//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" title="Major point!! example image" alt="Major point!! example image" style="display: block; margin: auto;" />
+
+
+### Video examples
+
+You can use `knitr::include_url()` like this:
+
+```{r}
+knitr::include_url("https://www.youtube.com/embed/VOCYL-FNbr0")
+```
+
+OR this works:
+
+<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px"></iframe>
+
+### Links to files
+
+This works:
+
+```{r, fig.align="center", echo=FALSE}
+knitr::include_url("https://www.messiah.edu/download/downloads/id/921/Microaggressions_in_the_Classroom.pdf", height = "800px")
+```
+
+Or this:
+
+[This works](https://www.messiah.edu/download/downloads/id/921/Microaggressions_in_the_Classroom.pdf).
+
+Or this:
+
+<iframe src="https://www.messiah.edu/download/downloads/id/921/Microaggressions_in_the_Classroom.pdf" width="672" height="800px"></iframe>
+
+### Links to websites
+
+Examples of including a website link.
+
+This works:
+
+```{r, fig.align="center"}
+knitr::include_url("https://yihui.org")
+```
+
+OR this:
+
+![Another link](https://yihui.org)
+
+OR this:
+
+<iframe src="https://yihui.org" width="672" height="400px"></iframe>
+
+### Citation examples
+
+We can put citations at the end of a sentence like this [@R-bookdown].
+Or multiple citations [@R-bookdown, @R-rmarkdown].
+
+but they need a ; separator [@R-bookdown, @R-rmarkdown].
+
+In text, we can put citations like this  @R-rmarkdown.
+
+## Print out session info
+
+```{r}
+sessionInfo()
+```

inst/extdata/_bookdown.yml

@@ -0,0 +1,13 @@
+book_filename: "Course_Name"
+chapter_name: "Chapter "
+repo: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/
+rmd_files: ["index.Rmd",
+            "01-intro.Rmd",
+            "02-example-chapter.Rmd"]
+new_session: yes
+bibliography: "references.bib"
+delete_merged_file: true
+language:
+  ui:
+    chapter_name: "Chapter"
+output_dir: "docs"

inst/extdata/index.Rmd

@@ -0,0 +1,6 @@
+---
+date: "`r format(Sys.time(), '%B, %Y')`"
+link-citations: yes
+---
+
+# About this Course

inst/extdata/references.bib

@@ -0,0 +1,85 @@
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2020},
+  url = {https://www.R-project.org/},
+}
+
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2021},
+  note = {https://github.com/rstudio/bookdown,
+https://pkgs.rstudio.com/bookdown/},
+}
+
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2021},
+  note = {R package version 1.33},
+  url = {https://yihui.org/knitr/},
+}
+
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2021},
+  note = {https://github.com/rstudio/rmarkdown,
+https://pkgs.rstudio.com/rmarkdown/},
+}
+
+@Book{bookdown2016,
+  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2016},
+  note = {ISBN 978-1138700109},
+  url = {https://bookdown.org/yihui/bookdown},
+}
+
+@Book{knitr2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {https://yihui.org/knitr/},
+}
+
+@InCollection{knitr2014,
+  booktitle = {Implementing Reproducible Computational Research},
+  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
+  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  year = {2014},
+  note = {ISBN 978-1466561595},
+  url = {http://www.crcpress.com/product/isbn/9781466561595},
+}
+
+@Book{rmarkdown2018,
+  title = {R Markdown: The Definitive Guide},
+  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2018},
+  note = {ISBN 9781138359338},
+  url = {https://bookdown.org/yihui/rmarkdown},
+}
+
+@Book{rmarkdown2020,
+  title = {R Markdown Cookbook},
+  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2020},
+  note = {ISBN 9780367563837},
+  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
+}
+