Merge pull request #246 from ThinkR-open/clean-obsolete-inflate

Clean obsolete files during inflate when possible
ThinkR-open · Apr 30, 2024 · efd0e79 · efd0e79
2 parents a3c26c9 + 029bd8b
commit efd0e79
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diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v3

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -44,7 +44,7 @@ Suggests:
     rmarkdown,
     rstudioapi,
     styler,
-    testthat (>= 3.0.0),
+    testthat (>= 3.2.0),
     withr
 VignetteBuilder: 
     knitr

diff --git a/NEWS.md b/NEWS.md
@@ -3,9 +3,11 @@
 ## Breaking changes
 
 - {fusen} now relies on {lightparser} instead of {parsermd} to parse flat file. This allows to avoid installation problems with {parsermd}, which is not updated anymore. As {lightparser} is lighter, this may have unattended effects on specific flat file cases. Please report any issue you may encounter. (#233)
+- `inflate_all*()` does not use parameter `clean` anymore. Use `check_unregistered` instead to check if all files are registered in the configuration file.
 
 ## New features
 
+- `inflate()` detects functions renamed or removed and allow to clean the package repository (#24)
 - Allow `organisation` in `init_share_on_github()` to send to a GitHub organisation
 - Fix `load_flat_functions()` to work with VSCode
 

diff --git a/R/fill_description.R b/R/fill_description.R
@@ -77,5 +77,5 @@ fill_description <- function(pkg = ".", fields, overwrite = FALSE) {
 
   desc$write(file = desc_file)
 
-  desc_file
+  invisible(desc_file)
 }
diff --git a/R/inflate.R b/R/inflate.R
@@ -24,6 +24,10 @@ regex_example <- paste(regex_example_vec, collapse = "|")
 #' @param document Logical. Whether to document your package using \code{\link[attachment:att_amend_desc]{att_amend_desc}}
 #' @param overwrite Logical (TRUE, FALSE) or character ("ask", "yes", "no).
 #' Whether to overwrite vignette and functions if already exists.
+#' @param clean Logical (TRUE, FALSE) or character ("ask", "yes", "no)
+#' Whether to delete files that are not anymore created by the current
+#'  flat file. Typically, if you have deleted or renamed a function
+#'  in the flat file. Default to "ask".
 #' @param ... Arguments passed to `devtools::check()`.
 #'     For example, you can do `inflate(check = TRUE, quiet = TRUE)`, where `quiet` is
 #'     passed to `devtools::check()`.
@@ -64,19 +68,23 @@ regex_example <- paste(regex_example_vec, collapse = "|")
 inflate <- function(pkg = ".", flat_file,
                     vignette_name = "Get started",
                     open_vignette = TRUE,
-                    check = TRUE, document = TRUE,
+                    check = TRUE,
+                    document = TRUE,
                     overwrite = "ask",
+                    clean = "ask",
                     ...) {
   if (!is.null(list(...)[["name"]])) {
     stop(paste0(
-      "The `name` argument to `inflate()` is deprecated since {fusen} version 0.3.0.",
+      "The `name` argument to `inflate()`",
+      " is deprecated since {fusen} version 0.3.0.",
       "\nPlease use `vignette_name = '", list(...)[["name"]], "'` instead.\n"
     ))
     vignette_name <- list(...)[["name"]]
   }
   if (!is.null(list(...)[["rmd"]])) {
     stop(paste0(
-      "The `rmd` argument to `inflate()` is deprecated since {fusen} version 0.3.0.",
+      "The `rmd` argument to `inflate()`",
+      " is deprecated since {fusen} version 0.3.0.",
       "\nPlease use `flat_file = '", list(...)[["rmd"]], "'` instead.\n"
     ))
     flat_file <- list(...)[["rmd"]]
@@ -92,21 +100,24 @@ inflate <- function(pkg = ".", flat_file,
   }
 
   # If flat_file empty
-  if (missing(flat_file) && requireNamespace("rstudioapi") && rstudioapi::isAvailable() &&
+  if (missing(flat_file) &&
+    requireNamespace("rstudioapi") && rstudioapi::isAvailable() &&
     rstudioapi::hasFun("getSourceEditorContext")) {
     curr_editor <- rstudioapi::getSourceEditorContext()
     current_file <- curr_editor$path
-    if (!is.null(current_file) && grepl("^flat.*[.](R|r|q)md$", basename(current_file))) {
+    if (!is.null(current_file) &&
+      grepl("^flat.*[.](R|r|q)md$", basename(current_file))) {
       if (overwrite == "ask") {
         sure <- paste0(
-          "You did not specify parameter 'flat_file'. The current file will be inflated:\n",
+          "You did not specify parameter 'flat_file'.",
+          " The current file will be inflated:\n",
           current_file, ".\n",
           "With vignette name: ", vignette_name, "\n",
           "Are you sure this is what you planned? (y/n)\n"
         )
-        do_it <- readline(sure) == "y"
+        do_it <- readline(sure) == "y" || readline(sure) == "yes"
       } else {
-        do_it <- isTRUE(overwrite)
+        do_it <- isTRUE(overwrite) || overwrite == "yes"
       }
       if (do_it) {
         message(
@@ -127,7 +138,10 @@ inflate <- function(pkg = ".", flat_file,
   }
 
   old <- setwd(pkg)
-  if (normalizePath(old, mustWork = FALSE) != normalizePath(pkg, mustWork = FALSE)) {
+  if (
+    normalizePath(old, mustWork = FALSE) !=
+      normalizePath(pkg, mustWork = FALSE)
+  ) {
     if (dir.exists(old)) {
       on.exit(setwd(old))
     } else {
@@ -136,7 +150,10 @@ inflate <- function(pkg = ".", flat_file,
   }
 
   old_proj <- usethis::proj_get()
-  if (normalizePath(old_proj, mustWork = FALSE) != normalizePath(pkg, mustWork = FALSE)) {
+  if (
+    normalizePath(old_proj, mustWork = FALSE) !=
+      normalizePath(pkg, mustWork = FALSE)
+  ) {
     if (dir.exists(old_proj)) {
       on.exit(usethis::proj_set(old_proj))
     } else {
@@ -151,16 +168,17 @@ inflate <- function(pkg = ".", flat_file,
 
   if (!file.exists(file.path(normalizePath(pkg), "DESCRIPTION"))) {
     stop(
-      "DESCRIPTION file does not exist in your directory:", normalize_path_winslash(pkg), ".\n",
-      "Have you run the content of the 'description' chunk of your {fusen} template?"
+      "DESCRIPTION file does not exist in your directory:",
+      normalize_path_winslash(pkg), ".\n",
+      "Have you run the content of the 'description'",
+      " chunk of your {fusen} template?"
     )
   }
 
   if (length(list.files(pkg, pattern = ".Rproj")) > 0) {
     if (!file.exists(".Rbuildignore")) {
       file.create(".Rbuildignore")
     }
-    # usethis::use_build_ignore(basename(flat_file))
     usethis::use_build_ignore(paste0(basename(pkg), ".Rproj"))
     usethis::use_build_ignore(".Rproj.user")
   }
@@ -173,7 +191,10 @@ inflate <- function(pkg = ".", flat_file,
   }
 
   if (!file.exists(flat_file_path)) {
-    stop(flat_file, " does not exists, please use fusen::add_flat_template() to create it.")
+    stop(
+      flat_file, " does not exists, ",
+      "please use fusen::add_flat_template() to create it."
+    )
   }
 
   # Are you sure ?
@@ -182,10 +203,14 @@ inflate <- function(pkg = ".", flat_file,
   }
   overwrite <- match.arg(overwrite, choices = c("ask", "yes", "no"))
   cleaned_vignette_name <- asciify_name(vignette_name)
-  vignette_path <- file.path(pkg, "vignettes", paste0(cleaned_vignette_name, ".Rmd"))
+  vignette_path <- file.path(
+    pkg, "vignettes",
+    paste0(cleaned_vignette_name, ".Rmd")
+  )
   if (file.exists(vignette_path)) {
     if (overwrite == "ask") {
-      rm_exist_vignette <- getFromNamespace("can_overwrite", "usethis")(vignette_path)
+      rm_exist_vignette <-
+        getFromNamespace("can_overwrite", "usethis")(vignette_path)
     } else {
       rm_exist_vignette <- ifelse(overwrite == "yes", TRUE, FALSE)
     }
@@ -242,14 +267,21 @@ inflate <- function(pkg = ".", flat_file,
 
   # Get functions and create R and tests files ----s
   if (!is.null(fun_code)) {
-    script_files <- create_functions_all(parsed_tbl, fun_code, pkg, relative_flat_file)
+    script_files <- create_functions_all(
+      parsed_tbl, fun_code, pkg, relative_flat_file
+    )
   } else {
-    message("No chunks named 'function-xx' or 'fun-xx' were found in the Rmarkdown file: ", flat_file)
+    message(
+      "No chunks named 'function-xx' or 'fun-xx'",
+      " were found in the Rmarkdown file: ", flat_file
+    )
     script_files <- tibble::tibble(type = character(0), path = character(0))
   }
 
   # Create vignette ----
-  if (!(is.null(vignette_name) || is.na(vignette_name) || vignette_name == "")) {
+  if (!(is.null(vignette_name) ||
+    is.na(vignette_name) ||
+    vignette_name == "")) {
     vignette_file <- create_vignette(
       parsed_tbl = parsed_tbl,
       pkg = pkg,
@@ -295,7 +327,7 @@ inflate <- function(pkg = ".", flat_file,
   config_file <- df_to_config(
     df_files = all_files,
     flat_file_path = relative_flat_file,
-    clean = TRUE,
+    clean = clean,
     state = "active",
     # TODO - Set to force = FALSE when there is a possibility to clean the config
     # when there are manually deleted file ----

diff --git a/R/inflate_all.R b/R/inflate_all.R
@@ -5,8 +5,14 @@
 #' Inflate all the flat files stored in "dev/" and starting with "flat_"
 #'
 #' @param pkg Path to package
-#' @param clean Logical. Whether to help detect unregistered files.
-#' @param stylers Function to be run at the end of the process, like `styler::style_pkg` or `lintr::lint_package` or a lambda function combining functions like: `function() {styler::style_pkg(); lintr::lint_package()}`. For a unique function, use the format without parenthesis `()` at the end of the command.
+#' @param check_unregistered Logical. Whether to help detect unregistered files.
+#' Typically files not created from a flat file and added manually in the repository.
+#' @param stylers Function to be run at the end of the process,
+#' like `styler::style_pkg` or `lintr::lint_package`
+#' or a lambda function combining functions like:
+#' `function() {styler::style_pkg(); lintr::lint_package()}`.
+#' For a unique function, use the format without parenthesis `()`
+#' at the end of the command.
 #' @inheritParams inflate
 #'
 #' @importFrom yaml read_yaml
@@ -15,16 +21,26 @@
 #'
 #' @return side effect. Inflates all your flat files that can be inflated.
 #'
-#' @details This requires to [inflate()] all flat files individually at least once, so that their specific inflate configurations are stored.
+#' @details This requires to [inflate()] all flat files
+#'  individually at least once, so that their specific
+#'  inflate configurations are stored.
 #'
-#' This also requires to register all R, tests and vignettes files of your package, even if not created with an inflate. Run [inflate_all()] once and read the messages. The first time, you will probably need to run [register_all_to_config()] if your package is not new.
+#' This also requires to register all R,
+#'  tests and vignettes files of your package,
+#' even if not created with an inflate.
+#' Run [inflate_all()] once and read the messages.
+#' The first time, you will probably need to run
+#' [register_all_to_config()] if your package is not new.
 #'
-#' For more information, read the `vignette("inflate-all-your-flat-files", package = "fusen")`
+#' For more information, read the
+#'  `vignette("inflate-all-your-flat-files", package = "fusen")`
 #'
 #' @seealso
 #'   [inflate()] for the options of a single file inflate,
-#'   [check_not_registered_files()] for the list of files not already associated with a flat file in the config file,
-#'   [register_all_to_config()] for automatically registering all files already present in the project before the first `inflate_all()`
+#'   [check_not_registered_files()] for the list of files
+#' not already associated with a flat file in the config file,
+#'   [register_all_to_config()] for automatically registering
+#' all files already present in the project before the first `inflate_all()`
 #'
 #' @export
 #' @examples
@@ -83,7 +99,14 @@
 #'
 #' # Clean the temporary directory
 #' unlink(dummypackage, recursive = TRUE)
-inflate_all <- function(pkg = ".", document = TRUE, check = TRUE, open_vignette = FALSE, overwrite = TRUE, clean = TRUE, stylers, ...) {
+inflate_all <- function(
+    pkg = ".",
+    document = TRUE,
+    check = TRUE,
+    open_vignette = FALSE,
+    overwrite = TRUE,
+    check_unregistered = TRUE,
+    stylers, ...) {
   config_file <- getOption("fusen.config_file", default = "dev/config_fusen.yaml")
 
   if (!file.exists(config_file)) {
@@ -120,7 +143,9 @@ inflate_all <- function(pkg = ".", document = TRUE, check = TRUE, open_vignette
     message("No flat files were inflated")
   } else {
     apply_inflate <- function(inflate_params, pkg, overwrite, open_vignette) {
-      config_file <- getOption("fusen.config_file", default = "dev/config_fusen.yaml")
+      config_file <- getOption("fusen.config_file",
+        default = "dev/config_fusen.yaml"
+      )
       # Change config option temporary, to be able to modify it on the fly
       config_file_tmp <- tempfile(pattern = "tempconfig")
       on.exit(file.remove(config_file_tmp))
@@ -140,10 +165,13 @@ inflate_all <- function(pkg = ".", document = TRUE, check = TRUE, open_vignette
       )
     }
 
-    apply_inflate(inflate_params, pkg = pkg, overwrite = overwrite, open_vignette = open_vignette)
+    apply_inflate(inflate_params,
+      pkg = pkg, overwrite = overwrite,
+      open_vignette = open_vignette
+    )
   }
 
-  if (isTRUE(clean)) {
+  if (isTRUE(check_unregistered)) {
     cli::cat_rule("check not registered files")
     invisible(check_not_registered_files(path = pkg))
   }
@@ -172,6 +200,6 @@ inflate_all <- function(pkg = ".", document = TRUE, check = TRUE, open_vignette
 
 #' @rdname inflate_all
 #' @export
-inflate_all_no_check <- function(pkg = ".", document = TRUE, open_vignette = FALSE, overwrite = TRUE, clean = TRUE, stylers, ...) {
-  inflate_all(pkg = pkg, document = document, check = FALSE, open_vignette = open_vignette, overwrite = overwrite, clean = clean, stylers, ...)
+inflate_all_no_check <- function(pkg = ".", document = TRUE, open_vignette = FALSE, overwrite = TRUE, check_unregistered = TRUE, stylers, ...) {
+  inflate_all(pkg = pkg, document = document, check = FALSE, open_vignette = open_vignette, overwrite = overwrite, check_unregistered = check_unregistered, stylers, ...)
 }