Merge pull request #33 from DanChaltiel/32-autoimport-option-for-cent…

…ralized-location

Option to add imports in the package-level documentation

NAMESPACE

@@ -34,9 +34,11 @@ importFrom(dplyr,transmute)
 importFrom(dplyr,ungroup)
 importFrom(fs,dir_create)
 importFrom(fs,file_create)
+importFrom(fs,file_delete)
 importFrom(fs,file_exists)
 importFrom(fs,file_move)
 importFrom(fs,path)
+importFrom(fs,path_abs)
 importFrom(fs,path_dir)
 importFrom(fs,path_temp)
 importFrom(glue,glue)
@@ -54,7 +56,10 @@ importFrom(purrr,map_depth)
 importFrom(purrr,map_int)
 importFrom(purrr,map_lgl)
 importFrom(purrr,walk)
+importFrom(readr,read_lines)
+importFrom(readr,write_lines)
 importFrom(rlang,caller_arg)
+importFrom(rlang,check_dots_empty)
 importFrom(rlang,check_installed)
 importFrom(rlang,current_env)
 importFrom(rlang,hash)

R/ai_parse.R

@@ -25,17 +25,17 @@ autoimport_parse = function(ref_list, cache_path, use_cache, pkg_name, ns,
     imap(function(refs, filename) {
       file_hash = hash_file(filename)
       filename = basename(filename)
-      if(verbose>1) cli_inform(c(">"="File {.file {filename}}"))
       cache_file = cache[[filename]]
       cache_file_hash = if(is.null(cache_file[["..file_hash"]])) "" else cache_file[["..file_hash"]]
       if(isTRUE(read_from_cache) && file_hash==cache_file_hash){
+        if(verbose>1) cli_inform(c(">"="Reading file {.file {filename}} (from cache)"))
         rtn_file = cache[[filename]][["..imports"]] %>%
           map(~{
             if(nrow(.x)>0) .x$ai_source = "cache_file"
             .x
           })
-        verb = "Reading from cache"
       } else {
+        if(verbose>1) cli_inform(c(">"="Reading file {.file {filename}} (from file)"))
         rtn_file = refs %>%
           imap(function(ref, fun_name){
             cache_ref = cache_file[[fun_name]]
@@ -54,14 +54,12 @@ autoimport_parse = function(ref_list, cache_path, use_cache, pkg_name, ns,
             }
             rtn_ref
           })
-        verb = "Reading from file"
         cache[[filename]][["..file_hash"]] <<- file_hash
         cache[[filename]][["..imports"]] <<- rtn_file
       }
       if(verbose>1){
         s = rtn_file %>% map_dbl(nrow) %>% sum()
-        cli_inform(c("!"=verb,
-                     "i"="Found {s} function{?s} to import in {length(rtn_file)}
+        cli_inform(c("i"="Found {s} function{?s} to import in {length(rtn_file)}
                      function{?s} or code chunk{?s}."))
       }
       rtn_file

R/ai_write.R

@@ -1,27 +1,73 @@
 
+
 #' Take a dataframe from `autoimport_ask()`, a reflist from `autoimport_read()`, and
 #' a list of lines from `readr::read_lines()`, and compute for each file what importFrom
 #' lines should be removed or inserted.
 #' Writes the correct lines in `target_dir` so they can be reviewed in `import_review()`.
 #' Returns nothing of use.
-#'
-#' @importFrom cli cli_h1 cli_inform
-#' @importFrom dplyr setdiff
-#' @importFrom fs path
-#' @importFrom purrr imap map
-#' @importFrom stringr str_ends
-#' @importFrom tibble tibble
 #' @noRd
 #' @keywords internal
-autoimport_write = function(data_imports, ref_list, lines_list, ignore_package,
-                            pkg_name, target_dir, verbose) {
-
-  if(verbose>0) cli_h1("Writing")
-  if(verbose>1) cli_inform(c(">"="Temporarily writing to {.path {target_dir}}."))
+#' @importFrom cli cli_h1 cli_inform
+#' @importFrom fs file_delete
+autoimport_write = function(data_imports, ref_list, lines_list, location,
+                            ignore_package, pkg_name, target_dir, verbose){
 
   stopifnot(is.data.frame(data_imports))
   stopifnot(is.character(data_imports$pkg))
   stopifnot(names(ref_list)==names(lines_list))
+  file_delete(dir(target_dir, full.names=TRUE))
+
+  if(location=="function"){
+    if(verbose>0) cli_h1("Writing at function level")
+    if(verbose>1) cli_inform(c(">"="Temporarily writing to {.path {target_dir}}."))
+    .autoimport_write_lvl_fn(data_imports, ref_list, lines_list,
+                             ignore_package, pkg_name, target_dir, verbose)
+  } else {
+    if(verbose>0) cli_h1("Writing at package level")
+    if(verbose>1) cli_inform(c(">"="Temporarily writing to {.path {target_dir}}."))
+    .autoimport_write_lvl_pkg(data_imports, ref_list, lines_list,
+                              ignore_package, pkg_name, target_dir, verbose)
+  }
+}
+
+
+#' @noRd
+#' @keywords internal
+#' @importFrom dplyr filter mutate
+#' @importFrom fs path
+#' @importFrom glue glue
+#' @importFrom stringr str_ends
+.autoimport_write_lvl_pkg = function(data_imports, ref_list, lines_list,
+                                     ignore_package, pkg_name, target_dir, verbose) {
+  #merge all functions inserts into one (by setting source_fun)
+  imports = data_imports |>
+    filter(!(ignore_package & str_ends(file, "-package.[Rr]"))) |>
+    mutate(source_fun="package_level") |>
+    get_inserts(exclude=c("base", "inner", pkg_name)) |>
+    unlist()
+  inserts = glue("#' @importFrom {imports}")
+
+  cur_package_doc = path("R", paste0(pkg_name, "-package"), ext="R")
+  new_package_doc = path(target_dir, paste0(pkg_name, "-package"), ext="R")
+
+  .copy_package_doc(cur_package_doc, new_package_doc)
+  .add_autoimport_package_doc(new_package_doc)
+  .update_package_doc(new_package_doc, inserts)
+  .remove_fun_lvl_imports(lines_list, target_dir, except=cur_package_doc)
+  TRUE
+}
+
+
+#' @noRd
+#' @keywords internal
+#' @importFrom cli cli_inform
+#' @importFrom dplyr setdiff
+#' @importFrom fs path
+#' @importFrom purrr imap map
+#' @importFrom stringr str_ends
+#' @importFrom tibble tibble
+.autoimport_write_lvl_fn = function(data_imports, ref_list, lines_list,
+                                    ignore_package, pkg_name, target_dir, verbose) {
 
   # data_imports %>% filter(fun=="writeLines")
   # .x %>% filter(fun=="writeLines")
@@ -76,6 +122,78 @@ autoimport_write = function(data_imports, ref_list, lines_list, ignore_package,
 }
 
 
+# Utils pkg-level -----------------------------------------------------------------------------
+
+
+#' @noRd
+#' @keywords internal
+#' @importFrom fs file_exists
+#' @importFrom readr read_lines write_lines
+.copy_package_doc = function(cur_package_doc, new_package_doc){
+  if(file_exists(cur_package_doc)){
+    write_lines(read_lines(cur_package_doc), file=new_package_doc)
+  }
+}
+
+#' @noRd
+#' @keywords internal
+#' @importFrom cli cli_inform
+#' @importFrom fs file_exists
+#' @importFrom readr read_lines write_lines
+#' @importFrom stringr str_detect
+.add_autoimport_package_doc = function(package_doc){
+  if(!file_exists(package_doc)){
+    cli_inform("Adding package-level documentation {.path {package_doc}}.")
+    content = ""
+  } else {
+    content = read_lines(package_doc)
+  }
+  if(any(str_detect(content, "autoimport namespace: start"))){
+    return(TRUE)
+  }
+
+  content = c(content, "",
+              "# The following block is used by autoimport.",
+              "## autoimport namespace: start",
+              "## autoimport namespace: end",
+              "NULL")
+  write_lines(content, package_doc)
+}
+
+#' @noRd
+#' @keywords internal
+#' @importFrom readr read_lines write_lines
+#' @importFrom stringr str_detect
+.update_package_doc = function(package_doc, inserts){
+  content = read_lines(package_doc)
+  start = str_detect(content, "autoimport namespace: start") |> which()
+  stop  = str_detect(content, "autoimport namespace: end")  |> which()
+  if(length(start)==0) start = length(content)
+  if(length(stop)==0)  stop = length(content)
+
+  new_content = c(content[1:start], inserts, content[stop:length(content)])
+  write_lines(new_content, package_doc)
+}
+
+#' remove all `@importFrom` tags from source
+#' @importFrom fs path path_abs
+#' @importFrom purrr imap
+#' @importFrom readr write_lines
+#' @importFrom stringr str_starts
+#' @noRd
+#' @keywords internal
+.remove_fun_lvl_imports = function(lines_list, target_dir, except){
+  lines_list |>
+    imap(function(lines, filename){
+      if(path_abs(filename) %in% path_abs(except)) return(FALSE)
+      target_file = path(target_dir, basename(filename))
+      rmv = str_starts(lines, "#+' *@importFrom")
+      new_lines = lines[!rmv]
+      write_lines(new_lines, target_file)
+      TRUE
+    })
+}
+
 # Utils ---------------------------------------------------------------------------------------
 
 
@@ -142,7 +260,7 @@ get_lines2 = function(src_ref, imports){
 }
 
 #' @param lines result of [read_lines()]
-#' @param insert line to insert
+#' @param insert lines to insert
 #' @param pos insert before this position
 #' @noRd
 #' @keywords internal

R/autoimport.R

@@ -2,15 +2,17 @@
 #' Automatically compute `@importFrom` tags
 #'
 #' Automatically read all `R` files and compute appropriate `@importFrom` tags in the roxygen headers.
-#' Choose which tags to add in the shiny app [import_review()] afterward.
+#' The tags can be added to the source files using the [import_review()] shiny app afterward.
 #'
 #' @param root Path to the root of the package.
+#' @param location Whether to add `@importFrom` dispatched above each function, or centralised at the package level.
 #' @param files Files to read. Default to the `R/` folder.
 #' @param namespace_file Path to the NAMESPACE file
 #' @param description_file Path to the DESCRIPTION file
 #' @param use_cache Whether to use the cache system. Can only be "read" or "write".
 #' @param ignore_package Whether to ignore files ending with `-package.R`
 #' @param verbose The higher, the more output printed. May slow the process a bit.
+#' @param ... unused
 #'
 #' @return Mostly used for side effects. Invisibly returns a dataframe summarizing the function imports, with input arguments as attributes.
 #' @export
@@ -29,16 +31,20 @@
 #' @importFrom dplyr setdiff
 #' @importFrom fs file_exists path path_dir
 #' @importFrom purrr map walk
-#' @importFrom rlang check_installed current_env set_names
+#' @importFrom rlang check_dots_empty check_installed current_env set_names
 #' @importFrom utils sessionInfo
 autoimport = function(root=".",
+                      ...,
+                      location=c("function", "package"),
                       files=get_R_dir(root),
                       namespace_file="NAMESPACE",
                       description_file="DESCRIPTION",
                       use_cache=TRUE, ignore_package=TRUE,
                       verbose=2){
   target_dir = get_target_dir()
+  check_dots_empty()
   ns = parse_namespace(namespace_file)
+  location = match.arg(location)
   importlist_path = getOption("autoimport_importlist", path(root, "inst/IMPORTLIST"))
   cache_path = get_cache_path(root)
   if(file_exists(path(root, namespace_file))) namespace_file = path(root, namespace_file)
@@ -74,7 +80,7 @@ autoimport = function(root=".",
 
   data_imports = autoimport_ask(data_imports, ns, importlist_path, verbose)
 
-  ai_write = autoimport_write(data_imports, ref_list, lines_list,
+  ai_write = autoimport_write(data_imports, ref_list, lines_list, location,
                               ignore_package, pkg_name, target_dir, verbose)
   if(verbose>0) cli_h1("Finished")
 

R/decision.R

@@ -20,21 +20,26 @@
 #' @source inspired by [testthat::snapshot_review()]
 #' @export
 #' @importFrom cli cli_inform
+#' @importFrom dplyr arrange desc
 #' @importFrom rlang check_installed
+#' @importFrom stringr str_ends
 import_review = function(source_path="R/",
                          output_path=get_target_dir(),
                          background=getOption("autoimport_background", FALSE)) {
   check_installed("shiny", "for `import_review()` to work")
   check_installed("diffviewer", "for `import_review()` to work")
-  data_files=review_files(source_path, output_path)
+  data_files = review_files(source_path, output_path) |>
+    arrange(desc(str_ends(old_files, "package.[Rr]")))
 
   if(!any(data_files$changed)){
     cli_inform("No changes to review.")
     return(invisible(FALSE))
   }
 
   go = function(data_files){
-    review_app(data_files)
+    data_files %>%
+      filter(changed) %>%
+      review_app()
     rstudio_tickle()
   }
 

inst/IMPORTLIST

@@ -1,6 +1,8 @@
 as_tibble = dplyr
 attr = base
+check_dots_empty = rlang
 desc = dplyr
+dir_create = fs
 div = shiny
 file_exists = fs
 filter = dplyr
@@ -12,11 +14,13 @@ ns_env = rlang
 order = base
 path = fs
 print = base
+read_lines = readr
 readLines = base
 regex = stringr
 set_names = rlang
 setdiff = base
 starts_with = dplyr
 unname = base
 which = base
+write_lines = readr
 writeLines = base

tests/testthat/helper-init.R

@@ -92,7 +92,7 @@ expect_not_imported = function(output, pkg, fun){
   invisible(faulty)
 }
 
-test_autoimport = function(files, bad_ns=FALSE, use_cache=FALSE, root=NULL, verbose=2){
+test_autoimport = function(files, bad_ns=FALSE, use_cache=FALSE, root=NULL, ..., verbose=2){
   #reset file paths
   if(is.null(root)){
     dir_source = test_path("source") %>% normalizePath()
@@ -124,7 +124,8 @@ test_autoimport = function(files, bad_ns=FALSE, use_cache=FALSE, root=NULL, verb
     ignore_package=TRUE,
     use_cache=use_cache,
     namespace_file=ns,
-    verbose=verbose
+    verbose=verbose,
+    ...
   )
 
 }