Merge pull request #166 from ThinkR-open/v0.4.1

chore: upgrade to 0.4.1

Author: statnmap

.github/workflows/R-CMD-check-HTML5.yaml

@@ -0,0 +1,42 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-HTML5
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_RD_VALIDATE_RD2HTML_: TRUE
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - name: Install tidy
+        run: sudo apt install tidy
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'devel'
+          http-user-agent: 'release'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--as-cran"'
+          build_args: 'character()'
+          error-on: '"note"'

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: fusen
-Title: Build a Package from Rmarkdown File
-Version: 0.4.0.9000
+Title: Build a Package from Rmarkdown Files
+Version: 0.4.1
 Authors@R: c(
     person("Sebastien", "Rochette", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1565-9313")),
     person("ThinkR", role = "cph")
   )
-Description: Use Rmarkdown First method to build your package.  Start your
+Description: Use Rmarkdown First method to build your package. Start your
     package with documentation, functions, examples and tests in the same
     unique file. Everything can be set from the Rmarkdown template file
-    provided in your project, then inflated as a package.  Inflating the
+    provided in your project, then inflated as a package. Inflating the
     template copies the relevant chunks and sections in the appropriate
     files required for package development.
 License: MIT + file LICENSE

NEWS.md

@@ -1,10 +1,14 @@
-# fusen (development version)
+# fusen 0.4.1
 
 ## New features
 
 - Load all `function` chunks of the flat file currently opened with `load_flat_functions()` (Like a `load_all()` for a flat file)
 - Allow to `inflate()` a Quarto ".qmd" flat file (#160)
 
+## Minor
+
+- Fix HTML5 doc
+
 # fusen 0.4.0
 
 ## New features

R/add_flat_template.R

@@ -2,53 +2,53 @@
 
 #' @rdname add_flat_template
 #' @export
-add_additional <- function(pkg = ".",
-                           dev_dir = "dev",
-                           flat_name = "additional",
-                           overwrite = FALSE,
-                           open = TRUE) {
+add_additional <- function(
+    pkg = ".", 
+    dev_dir = "dev",
+    flat_name = "additional",
+    overwrite = FALSE,
+    open = TRUE) {
   add_flat_template(
     template = "additional",
-    pkg = pkg,
+    pkg = pkg, 
     dev_dir = dev_dir,
     flat_name = flat_name,
     overwrite = overwrite,
-    open = open
-  )
+    open = open) 
 }
 
 #' @rdname add_flat_template
 #' @export
-add_minimal <- function(pkg = ".",
-                        dev_dir = "dev",
-                        flat_name = "minimal",
-                        overwrite = FALSE,
-                        open = TRUE) {
+add_minimal <- function(
+    pkg = ".", 
+    dev_dir = "dev",
+    flat_name = "minimal",
+    overwrite = FALSE,
+    open = TRUE) {
   add_flat_template(
     template = "minimal",
-    pkg = pkg,
+    pkg = pkg, 
     dev_dir = dev_dir,
     flat_name = flat_name,
     overwrite = overwrite,
-    open = open
-  )
+    open = open) 
 }
 
 #' @rdname add_flat_template
 #' @export
-add_full <- function(pkg = ".",
-                     dev_dir = "dev",
-                     flat_name = "full",
-                     overwrite = FALSE,
-                     open = TRUE) {
+add_full <- function(
+    pkg = ".", 
+    dev_dir = "dev",
+    flat_name = "full",
+    overwrite = FALSE,
+    open = TRUE) {
   add_flat_template(
     template = "full",
-    pkg = pkg,
+    pkg = pkg, 
     dev_dir = dev_dir,
     flat_name = flat_name,
     overwrite = overwrite,
-    open = open
-  )
+    open = open) 
 }
 
 #' Add flat Rmd file that drives package development
@@ -59,7 +59,7 @@ add_full <- function(pkg = ".",
 #' @param open Logical. Whether to open file after creation
 #' @param dev_dir Name of directory for development Rmarkdown files. Default to "dev".
 #' @param flat_name Name of the file to write in dev.
-#' Use the name of the main function of your template to get chunks pre-filled with this function name.
+#' Use the name of the main function of your template to get chunks pre-filled with this function name. 
 #'
 #' @importFrom tools file_path_sans_ext
 #' @details
@@ -76,7 +76,7 @@ add_full <- function(pkg = ".",
 #'
 #' Abbreviated names can also be used for the different templates:
 #' "add" for additional, "min" for minimal, "teach" for teaching, "dev" for "dev_history".
-#'
+#' 
 #' `add_additional()`, `add_minimal()`, `add_full()` are wrapper around `add_flat_template("additional")`, ...
 #' However, `add_dev_history()` is a deprecated function from a previous version.
 #'
@@ -89,67 +89,62 @@ add_full <- function(pkg = ".",
 #' # Create a new project
 #' dummypackage <- tempfile("dummypackage")
 #' dir.create(dummypackage)
-#'
+#' 
 #' # Add
 #' add_flat_template(template = "teaching", pkg = dummypackage)
 #' # Delete dummy package
 #' unlink(dummypackage, recursive = TRUE)
-#'
+#' 
 #' # For classical use in your package
 #' \dontrun{
 #' # first time ever using 'fusen'
-#' add_flat_template("full")
-#'
+#' add_flat_template("full") 
+#' 
 #' # first time in your new package
 #' add_flat_template("minimal")
-#'
+#' 
 #' # add new flat file for new functions
 #' add_flat_template("add")
-#'
+#' 
 #' # add new flat template for teaching (a reduced full template)
 #' add_flat_template("teaching")
-#' #'
-#' }
-add_flat_template <- function(template = c("full", "minimal", "additional", "teaching", "dev_history"),
-                              pkg = ".",
-                              dev_dir = "dev",
-                              flat_name = template,
-                              overwrite = FALSE,
-                              open = TRUE) {
+#' #'}
+add_flat_template <- function(
+    template = c("full", "minimal", "additional", "teaching", "dev_history"),
+    pkg = ".", 
+    dev_dir = "dev",
+    flat_name = template,
+    overwrite = FALSE,
+    open = TRUE) {
+  
   project_name <- get_pkg_name(pkg = pkg)
-
+  
   if (project_name != asciify_name(project_name, to_pkg = TRUE)) {
-    stop(
-      "Please rename your project/directory with: `", asciify_name(project_name, to_pkg = TRUE),
-      "` as a package name should only contain letters, numbers and dots."
-    )
+    stop("Please rename your project/directory with: `", asciify_name(project_name, to_pkg = TRUE),
+         "` as a package name should only contain letters, numbers and dots.")
   }
-
+  
   template <- match.arg(template)
-  if (!template %in% c("full", "teaching", "dev_history") &
-    !flat_name %in% c("minimal", "additional")) {
+  if (!template %in% c("full", "teaching", "dev_history")
+      & !flat_name %in% c("minimal", "additional")) {
     fun_name <- gsub("-", "_", asciify_name(flat_name))
   } else {
     fun_name <- NA
   }
-  flat_name <- paste0(
-    "flat_",
-    asciify_name(gsub("[.]Rmd$", "", flat_name[1])), ".Rmd"
-  )
-
+  flat_name <- paste0("flat_", 
+                      asciify_name(gsub("[.]Rmd$", "", flat_name[1])), ".Rmd")
+  
   pkg <- normalizePath(pkg)
   full_dev_dir <- file.path(pkg, dev_dir)
-  if (!dir.exists(full_dev_dir)) {
-    dir.create(full_dev_dir)
-  }
-  dev_file_path <- file.path(full_dev_dir, flat_name) # "dev_history.Rmd")
-
+  if (!dir.exists(full_dev_dir)) {dir.create(full_dev_dir)}
+  dev_file_path <- file.path(full_dev_dir, flat_name) #"dev_history.Rmd")
+  
   # Which template ----
   if (template == "dev_history") {
     dev_file_path <- character(0)
   } else {
     template_file <- system.file(paste0("flat-template-", template, ".Rmd"), package = "fusen")
-
+    
     if (file.exists(dev_file_path) & overwrite == FALSE) {
       n <- length(list.files(full_dev_dir, pattern = "^flat_.*[.]Rmd"))
       dev_file_path <- file.path(full_dev_dir, paste0(file_path_sans_ext(flat_name), "_", n + 1, ".Rmd"))
@@ -160,50 +155,40 @@ add_flat_template <- function(template = c("full", "minimal", "additional", "tea
       )
     }
     dev_name <- basename(dev_file_path)
-
+    
     # Change lines asking for pkg name
     lines_template <- readLines(template_file)
-
+    
     lines_template[grepl("<my_package_name>", lines_template)] <-
-      gsub(
-        "<my_package_name>", project_name,
-        lines_template[grepl("<my_package_name>", lines_template)]
-      )
-
+      gsub("<my_package_name>", project_name,
+           lines_template[grepl("<my_package_name>", lines_template)])
+    
     # Change flat_template file name
     # _inflate
     lines_template[grepl("dev/flat_template.Rmd", lines_template)] <-
-      gsub(
-        "dev/flat_template.Rmd", file.path(dev_dir, dev_name),
-        lines_template[grepl("dev/flat_template.Rmd", lines_template)]
-      )
+      gsub("dev/flat_template.Rmd", file.path(dev_dir, dev_name),
+           lines_template[grepl("dev/flat_template.Rmd", lines_template)])
     # _title
     lines_template[grepl("flat_template.Rmd", lines_template)] <-
-      gsub(
-        "flat_template.Rmd", dev_name,
-        lines_template[grepl("flat_template.Rmd", lines_template)]
-      )
-
+      gsub("flat_template.Rmd", dev_name,
+           lines_template[grepl("flat_template.Rmd", lines_template)])
+    
     # Change my_fun to fun_name
     if (!is.na(fun_name)) {
       lines_template[grepl("my_fun", lines_template)] <-
-        gsub(
-          "my_fun", fun_name,
-          lines_template[grepl("my_fun", lines_template)]
-        )
+        gsub("my_fun", fun_name,
+             lines_template[grepl("my_fun", lines_template)])
     }
-
+    
     cat(enc2utf8(lines_template), file = dev_file_path, sep = "\n")
   }
-
+  
   # Add the-dev-history when needed ----
   if (template %in% c("full", "minimal", "dev_history")) {
     dev_file <- file.path(full_dev_dir, "0-dev_history.Rmd")
     if (file.exists(dev_file) & !isTRUE(overwrite)) {
-      message(
-        "'0-dev_history.Rmd' already exists. It was not overwritten. ",
-        "Set `add_flat_template(overwrite = TRUE)` if you want to do so."
-      )
+      message("'0-dev_history.Rmd' already exists. It was not overwritten. ",
+              "Set `add_flat_template(overwrite = TRUE)` if you want to do so.")
     } else {
       copy <- file.copy(
         system.file("the-dev-history.Rmd", package = "fusen"),
@@ -215,8 +200,9 @@ add_flat_template <- function(template = c("full", "minimal", "additional", "tea
       }
       dev_file_path <- c(dev_file_path, dev_file)
     }
+    
   }
-
+  
   # Add data for the full template exemple
   if (template %in% c("full")) {
     inst_dir <- file.path(pkg, "inst")
@@ -227,15 +213,15 @@ add_flat_template <- function(template = c("full", "minimal", "additional", "tea
     # Example dataset
     file.copy(system.file("nyc_squirrels_sample.csv", package = "fusen"), inst_dir)
   }
-
+  
   # .Rbuildignore ----
   # usethis::use_build_ignore(dev_dir) # Cannot be used outside project
   if (length(list.files(pkg, pattern = "[.]Rproj")) == 0) {
     lines <- c(paste0("^", dev_dir, "$"), "^\\.here$")
   } else {
     lines <- c(paste0("^", dev_dir, "$"))
   }
-
+  
   buildfile <- normalizePath(file.path(pkg, ".Rbuildignore"), mustWork = FALSE)
   if (!file.exists(buildfile)) {
     existing_lines <- ""
@@ -247,11 +233,11 @@ add_flat_template <- function(template = c("full", "minimal", "additional", "tea
     all <- c(existing_lines, new)
     cat(enc2utf8(all), file = buildfile, sep = "\n")
   }
-
+  
   # Add a gitignore file in dev_dir ----
   # Files to ignore
-  lines <- c("*.html")
-
+  lines <- c("*.html", "*.R")
+  
   gitfile <- normalizePath(file.path(full_dev_dir, ".gitignore"), mustWork = FALSE)
   if (!file.exists(gitfile)) {
     existing_lines <- ""
@@ -263,13 +249,11 @@ add_flat_template <- function(template = c("full", "minimal", "additional", "tea
     all <- c(existing_lines, new)
     cat(enc2utf8(all), file = gitfile, sep = "\n")
   }
-
+  
   if (length(list.files(pkg, pattern = "[.]Rproj")) == 0) {
     here::set_here(pkg)
   }
-  if (isTRUE(open) & interactive()) {
-    usethis::edit_file(dev_file_path)
-  }
-
+  if (isTRUE(open) & interactive()) {usethis::edit_file(dev_file_path)}
+  
   dev_file_path
 }