* maintenance tasks

---

- avoid `dplyr::if_else()` in non-vectorized use
- improve source Rmd structure
- update min R version and use native pipe op in examples
- update lintr config
- update TODOs
- other small changes and fixes

Author: salim-b

.lintr

@@ -1,17 +1,17 @@
 # deviations from lintr's defaults only! to list all linter names enabled by default, use: `names(lintr::default_linters)`
 
-linters: with_defaults(absolute_path_linter = absolute_path_linter,
-                       implicit_integer_linter = implicit_integer_linter,
+linters: with_defaults(absolute_path_linter = absolute_path_linter(),
+                       implicit_integer_linter = implicit_integer_linter(),
                        line_length_linter = line_length_linter(160),
-                       nonportable_path_linter = nonportable_path_linter,
+                       nonportable_path_linter = nonportable_path_linter(),
                        object_length_linter = lintr::object_length_linter(40),
-                       semicolon_terminator_linter = semicolon_terminator_linter,
-                       todo_comment_linter = todo_comment_linter,
+                       semicolon_terminator_linter = semicolon_terminator_linter(),
+                       todo_comment_linter = todo_comment_linter(),
                        trailing_whitespace_linter = NULL,
-                       T_and_F_symbol_linter = T_and_F_symbol_linter,
-                       undesirable_function_linter = undesirable_function_linter,
+                       T_and_F_symbol_linter = T_and_F_symbol_linter(),
+                       undesirable_function_linter = undesirable_function_linter(),
                        undesirable_operator_linter = undesirable_operator_linter(c(lintr:::default_undesirable_operators, `->` = NA)),
-                       unneeded_concatenation_linter = unneeded_concatenation_linter)
+                       unneeded_concatenation_linter = unneeded_concatenation_linter())
 exclusions: c(list.files(path = "R",
                          recursive = TRUE,
                          full.names = TRUE,

DESCRIPTION

@@ -19,7 +19,7 @@ License: AGPL (>= 3)
 URL: https://gitlab.com/salim_b/r/pkgs/tocr
 BugReports: https://gitlab.com/salim_b/r/pkgs/tocr/issues
 Depends:
-    R (>= 3.4.4)
+    R (>= 4.1)
 Imports:
     checkmate (>= 1.8.5),
     curl (>= 4.3),
@@ -41,4 +41,4 @@ Remotes:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2

R/tocr-GEN.R R/tocr.gen.R

@@ -1,5 +1,16 @@
 # DO NOT EDIT THIS FILE BY HAND! Instead edit the R Markdown source file `Rmd/tocr.Rmd` and run `pkgpurl::purl_rmd()`.
-# See `README.md#r-markdown-format` for more information on the literature programming approach used applying the R Markdown format.
+# See `README.md#r-markdown-format` for more information on the literate programming approach used applying the R Markdown format.
+
+# tocr: TOC Generation for (R) Markdown Documents
+# Copyright (C) 2022 Salim Brüggemann
+# 
+# This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or any later version.
+# 
+# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
+# 
+# You should have received a copy of the GNU Affero General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
 
 utils::globalVariables(names = c("."))
 
@@ -23,9 +34,9 @@ get_non_code_block_indices <- function(md_lines) {
         # code block ends?
         if (stringr::str_detect(string = md_lines[[i]],
                                 pattern = paste0("^ {0,3}",
-                                                 dplyr::if_else(is_tilde, "~", "`"),
+                                                 ifelse(is_tilde, "~", "`"),
                                                  "{", nr_of_fence_chars, ",} *$"))) {
-          is_inside_code_block %<>% not()
+          is_inside_code_block %<>% magrittr::not()
         }
 
       } else {
@@ -38,7 +49,7 @@ get_non_code_block_indices <- function(md_lines) {
                                           pattern = "^ {0,3}~{3,}")
 
           nr_of_fence_chars <- stringr::str_count(string = md_lines[i],
-                                                  pattern = dplyr::if_else(is_tilde, "~", "`"))
+                                                  pattern = ifelse(is_tilde, "~", "`"))
         } else {
 
           non_code_block_indices %<>% c(i)
@@ -198,19 +209,19 @@ evaluate_position <- function(position,
 
   } else if (position == "above") {
 
-    position <- dplyr::if_else(min_tier == 1L,
-                               1L,
-                               stringr::str_which(string = md_lines,
-                                                  pattern = paste0("^ {0,3}#{", min_tier, ",6}\\s+\\S")) %>%
-                                 dplyr::first() %>%
-                                 ifelse(is.na(.), 2L, .) %>%
-                                 magrittr::subtract(1L) %>%
-                                 seq(from = 1L) %>%
-                                 magrittr::extract(md_lines, .) %>%
-                                 stringr::str_which(pattern = paste0("^ {0,3}#{1,", min_tier, "}\\s+\\S")) %>%
-                                 dplyr::last() %>%
-                                 ifelse(is.na(.), 0L, .) %>%
-                                 magrittr::add(1L))
+    position <- ifelse(min_tier == 1L,
+                       1L,
+                       stringr::str_which(string = md_lines,
+                                          pattern = paste0("^ {0,3}#{", min_tier, ",6}\\s+\\S")) %>%
+                         dplyr::first() %>%
+                         ifelse(is.na(.), 2L, .) %>%
+                         magrittr::subtract(1L) %>%
+                         seq(from = 1L) %>%
+                         magrittr::extract(md_lines, .) %>%
+                         stringr::str_which(pattern = paste0("^ {0,3}#{1,", min_tier, "}\\s+\\S")) %>%
+                         dplyr::last() %>%
+                         ifelse(is.na(.), 0L, .) %>%
+                         magrittr::add(1L))
 
   } else if (position == "below") {
 
@@ -405,9 +416,9 @@ process_md <- function(md_lines,
         stringr::str_replace_all(pattern = paste0("\\[[^\\]]*?\\]\\(#(",
                                                   toc_id, "|",
                                                   old_toc_id,
-                                                  dplyr::if_else(is_header_title,
-                                                                 "",
-                                                                 paste0("|", new_toc_id)),
+                                                  ifelse(is_header_title,
+                                                         "",
+                                                         paste0("|", new_toc_id)),
                                                   ")-*?\\) ?"),
                                  replacement = "") %>%
         # remove all anchor links where the link text is no longer than 2 chars
@@ -462,9 +473,9 @@ process_md <- function(md_lines,
           magrittr::subtract(min_tier - 1L)
 
         # update enumeration for ordered list TOC
-        enumeration <- dplyr::if_else(tier == previous_tier,
-                                      enumeration + 1L,
-                                      1L)
+        enumeration <- ifelse(tier == previous_tier,
+                              enumeration + 1L,
+                              1L)
 
         # update TOC data
         toc_data %<>% dplyr::add_row(tier = tier,
@@ -564,15 +575,16 @@ process_md <- function(md_lines,
 #' @export
 #'
 #' @examples
-#' library(magrittr)
-#'
-#' "https://raw.githubusercontent.com/ropensci/pdftools/e7248d9956c7e73968628fa3a8ed37f0a8c23b37/README.md" %>%
-#'   add_toc(position = 9) %>%
+#' md <- paste0("https://raw.githubusercontent.com/ropensci/pdftools/",
+#'              "e7248d9956c7e73968628fa3a8ed37f0a8c23b37/README.md")
+#' 
+#' md |>
+#'   tocr::add_toc(position = 9) |>
 #'   cat(sep = "\n")
 #' 
-#' add_toc(md = "https://raw.githubusercontent.com/ropensci/pdftools/e7248d9956c7e73968628fa3a8ed37f0a8c23b37/README.md",
-#'         listing_style = "ordered") %>%
-#'   readr::write_lines(path = "rmarkdown_README_incl_TOC.md")
+#' md |>
+#'   tocr::add_toc(listing_style = "ordered") |>
+#'   cat(sep = "\n")
 add_toc <- function(md,
                     min_tier = 2L,
                     max_tier = 6L,
@@ -582,7 +594,7 @@ add_toc <- function(md,
                     title = "Table of contents",
                     title_tier = min_tier,
                     add_backlinks = add_title,
-                    backlink_strings = c("\U1F805", "\U1F807"),
+                    backlink_strings = c("\u2191", "\u2193"),
                     backlink_position = c("before", "after"),
                     listing_style = c("-", "*", "ordered", "indented"),
                     toc_id = "toc",
@@ -743,15 +755,14 @@ add_toc <- function(md,
                                   filename = basename(md))
 
   # determine fallback HTML <id> attribute position for backlinks (ID of next header line above the TOC if existing)
-  fallback_id_position <-
-    dplyr::if_else(position > 1L,
-                   stringr::str_which(string = md_lines[1L:(min(length(md_lines), max(position - 1L, 1L)))],
-                                      pattern = "^ {0,3}#{1,6}\\s+\\S") %>%
-                     dplyr::last() %>%
-                     # if no header lines above TOC found, set to -1
-                     dplyr::if_else(is.na(.), -1L, .),
-                   # if `position` is 1 (or "none") there can't be any header lines above TOC
-                   1L)
+  fallback_id_position <- ifelse(position > 1L,
+                                 stringr::str_which(string = md_lines[1L:(min(length(md_lines), max(position - 1L, 1L)))],
+                                                    pattern = "^ {0,3}#{1,6}\\s+\\S") %>%
+                                   dplyr::last() %>%
+                                   # if no header lines above TOC found, set to -1
+                                   ifelse(is.na(.), -1L, .),
+                                 # if `position` is 1 (or "none") there can't be any header lines above TOC
+                                 1L)
 
   # determine if TOC title is a header or not
   is_header_title <- is.numeric(title_tier)
@@ -768,18 +779,19 @@ add_toc <- function(md,
     )
 
   # set position of new TOC ID
-  new_toc_id_position <- dplyr::if_else(use_fallback,
-                                        fallback_id_position,
-                                        as.integer(position))
+  new_toc_id_position <- ifelse(use_fallback,
+                                fallback_id_position,
+                                as.integer(position))
 
   # generate actual TOC ID if `position != "none"` (ensure it's unique)
   if (new_toc_id_position > 0L) {
 
     ## get all header texts preceding `new_toc_id_position` (to avoid duplicates)
     preceding_anchor_links <-
       # extract all header lines until `new_toc_id_position`
-      stringr::str_subset(string = md_lines[1L : dplyr::case_when(use_fallback ~ new_toc_id_position,
-                                                                  TRUE ~ as.integer(new_toc_id_position - 1L))],
+      stringr::str_subset(string = md_lines[1:ifelse(use_fallback,
+                                                     new_toc_id_position,
+                                                     new_toc_id_position - 1L)],
                           pattern = "^ {0,3}#{1,6}\\s+\\S") %>%
       # remove leading hashtags
       stringr::str_replace(pattern = "^ *#+",
@@ -1011,11 +1023,10 @@ add_toc <- function(md,
 #' @export
 #' 
 #' @examples
-#' library(magrittr)
-#' 
-#' remove_toc(md = paste0("https://raw.githubusercontent.com/thlorenz/doctoc/",
-#'                        "1d386261972d35c6bcd187d0a00e666f9d893d8d/README.md")) %>%
-#'   cat(sep = "\n")
+#' \dontrun{
+#' tocr::remove_toc(md = paste0("https://raw.githubusercontent.com/thlorenz/doctoc/",
+#'                              "1d386261972d35c6bcd187d0a00e666f9d893d8d/README.md")) |>
+#'   cat(sep = "\n")}
 remove_toc <- function(md,
                        old_toc_id = "toc") {
   add_toc(md = md,