add new functions render_all_rmd_project() and an addin that uses it

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioDataScience
 Type: Package
-Version: 2021.1.0
+Version: 2021.2.0
 Title: Configuration for Biological Data Science Course
 Description: User sign in and sign out for the Biological Data Science courses
   at the University of Mons, Belgium.
@@ -11,8 +11,8 @@ Authors@R: c(
   email = "guyliann.engels@umons.ac.be"))
 Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
 Depends: R (>= 3.5.0)
-Imports: learnitdown
-Suggests: covr, knitr, rmarkdown, testthat
+Imports: learnitdown, rmarkdown, rprojroot, shiny, miniUI, rstudioapi
+Suggests: covr, knitr, testthat
 Remotes: SciViews/learnitdown
 License: MIT + file LICENSE
 LazyData: true

NAMESPACE

@@ -1,7 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
 export(config)
+export(corr_rmd)
 export(obfuscator)
+export(render_sdd)
 export(sdd_info)
 export(sign_in)
 export(sign_out)
+import(rmarkdown)
+import(rprojroot)

NEWS.md

@@ -1,3 +1,9 @@
+# BioDataScience 2021.2.0
+
+- `render_sdd()` function convert a Rmarkdown files to html document with specific arguments.
+- `corr_rmd()` function is used to try to convert all Rmarkdown files in a project to html documents. If a document does not compile, a copy is created.
+- `Check my project` addin is an Rstudio addin used to validate several criteria on a project like the compilation of Rmarkdown.
+
 # BioDataScience 2021.1.0
 
 - `sdd_info()` function and corresponfing RStudio addin are introduced for easily sharing small pieces of text in a central repository.

R/addins.R

@@ -5,3 +5,49 @@ sdd_info_addin <- function()
 
 sign_out_addin <- function()
   sign_out()
+
+check_project_addin <- function() {
+
+  ui <- miniUI::miniPage(
+    miniUI::gadgetTitleBar("Check my project"),
+    miniUI::miniContentPanel(
+      shiny::h4("Project path"),
+      shiny::textOutput("proj_dir"),
+      shiny::h4("Convert to HTML documents all Rmarkdown documents in the project"),
+      shiny::tableOutput("render"),
+      shiny::hr()
+    )
+    )
+
+  server <- function(input, output, session) {
+
+    res_proj <- rprojroot::find_root(rprojroot::is_rstudio_project, path = ".")
+    res <- BioDataScience::corr_rmd(".", correction = FALSE)
+
+    output$proj_dir <- shiny::renderText({
+      print(res_proj)
+    })
+
+    output$render <- shiny::renderTable({
+        res
+      })
+
+    shiny::observeEvent(input$done, {
+      res1 <- res[res$check == "ERROR", ]
+
+      if(nrow(res1)>0)
+        rstudioapi::navigateToFile(res1$file) ## open files that do not knit
+
+      shiny::stopApp()
+    })
+
+    shiny::observeEvent(input$cancel, {
+      shiny::stopApp()
+    })
+
+  }
+
+  viewer <- shiny::paneViewer(300)
+  shiny::runGadget(ui, server, viewer = viewer)
+
+}

R/corr_rmd.R

@@ -0,0 +1,55 @@
+#' Convert to HTML documents all Rmarkdown in a project
+#'
+#'Find all R markdown files in a Rstudio project
+#'and try to convert then an HTML document with \code{render_sdd()}.
+#'
+#' @param path the path of the project
+#' @param correction If correction is TRUE, a copy of rmd file do not convert is created.
+#'
+#' @import rprojroot
+#'
+#' @return  a data.frame with the results of the compilations in html
+#' @export
+#'
+#' @examples
+#' #library(pfunctions)
+#' #test <- corr_project()
+#'
+corr_rmd <- function(path = ".", correction = TRUE) {
+
+  # Check if us a rstuio project
+  rprojroot::find_root(rprojroot::is_rstudio_project, path = path)
+
+  # Find all rmd files
+  paths <- list.files(path = path, pattern = "*.Rmd", recursive = TRUE)
+  paths_lg <- length(paths)
+
+  res <- data.frame(
+    "file" = vector("character", paths_lg),
+    "check" = vector("character", paths_lg),
+    "result" = vector("character", paths_lg)
+  )
+
+  for(i in seq_along(paths)) {
+    rmd_res <- try(render_sdd(paths[i]),
+      silent = TRUE)
+
+    rmd_res1 <- list(
+      "file" = paths[i] ,
+      "check" = ifelse(class(rmd_res) == "try-error", yes = "ERROR", no = "OK"),
+      "result" = as.character(rmd_res))
+
+    res[i, ] <- rmd_res1
+  }
+
+  if(isTRUE(correction)) {
+    res1 <- res[res$check == "ERROR",]
+
+    if(nrow(res1)>0) {
+      res1$file_corr <-gsub(".Rmd$", "_corr.Rmd", x = res1$file)
+    }
+      file.copy(from = res1$file, to = res1$file_corr)
+  }
+
+  return(res)
+}

R/render_all_rmd_project.R

@@ -0,0 +1,26 @@
+#' Convert to HTML documents an Rmarkdown with specific rules
+#'
+#' Convert Rmarkdown file in an HTML document a serie of predefined arguments
+#' in order to meet the requirements of the biological data science course.
+#' This functions use \code{render()} and \code{html_document()}
+#'
+#'
+#' @param path the path of the Rmd file.
+#' @param ... The arguments of render()
+#'
+#' @import rmarkdown
+#'
+#' @return  an html document
+#' @export
+#'
+#' @examples
+#' #library(pfunctions)
+#' #test <- render_sdd(path = "file.Rmd")
+#'
+render_sdd <- function(path, ...){
+  rmarkdown::render(path,
+      output_format = rmarkdown::html_document(
+        toc = TRUE, number_sections = TRUE, code_folding = "hide",
+        anchor_sections = TRUE, self_contained = FALSE), quiet = TRUE,...)
+}
+

inst/rstudio/addins.dcf

@@ -7,3 +7,8 @@ Name: Sign out
 Description: Sign out current user
 Binding: sign_out_addin
 Interactive: true
+
+Name: Check my project
+Description: Check my data science project
+Binding: check_project_addin
+Interactive: true