Merge branch 'main' into roxy-parse

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

@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
 
 permissions: read-all
 

.github/workflows/pkgdown.yaml

@@ -9,7 +9,7 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
 
 permissions: read-all
 

.github/workflows/test-coverage.yaml

@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
 
 permissions: read-all
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: reuseme
 Title: Collections of Utility Functions to Work Across Projects
-Version: 0.0.2.9005
+Version: 0.0.2.9006
 Authors@R: 
     person("Olivier", "Roy", , "olivierroy71@hotmail.com", role = c("aut", "cre"))
 Description: Allows you to browse current projects, rename files safely,
@@ -45,4 +45,4 @@ Suggests:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NEWS.md

@@ -17,6 +17,9 @@ that will passed on to `proj_list()`
 
 * `file_outline()` result is now a simpler data frame. The cli links are now created in the print method. (which makes more sense for truncation)
 
+* `use_todo("global::todo")` no longer works out of the box. You need to set `options(reuseme.global_todo = fs::path("Documents"))` explicitly (in .Rprofile) for example to make sure 
+  reuseme can write in a directory.
+
 ## Fixes
 
 * `rename_files2()` now looks in `.Rbuildignore` to see if some files should be replaced.
@@ -51,6 +54,8 @@ that will passed on to `proj_list()`
 
 * Package versions in NEWS.md are now normalized to yield better results.
 
+* `active_rs_doc()` returns the relative path if in RStudio project.
+
 # reuseme 0.0.2
 
 * `complete_todo()` no longer deletes the full line. It only deletes what it says it deletes (#27).

R/open.R

@@ -57,6 +57,14 @@ active_rs_doc <- function() {
     cli::cli_abort("Either RStudio is not available or you are trying to map an unsaved file")
   })
   path <- fs::path_expand_r(path)
+  active_proj <- proj_get2()
+  if (is.null(active_proj)) {
+    return(invisible(path))
+  }
+  if (isTRUE(fs::path_has_parent(path, active_proj))) {
+    path <- fs::path_rel(path)
+  }
+  path
   # likely not hapenning on RStudio >= 2023.06.2
 }
 

R/outdated-pkgs.R

@@ -22,12 +22,17 @@ outdated_pkgs <- function(type = c("binary", "source")) {
     default_repo <- getOption("repos")[[1]]
     default_repo <- sub("/$", "", default_repo)
     default_repo <- sub("https://", "", default_repo, fixed = TRUE)
+    if (!grepl("packagemanager", default_repo)) {
+      # ppm is not well detected
+      access_repo <- tryCatch(curl::nslookup(default_repo),
+                              error = function(e) {
+                                FALSE
+                              }
+      )
+    } else {
+      access_repo <- TRUE
+    }
 
-    access_repo <- tryCatch(curl::nslookup(default_repo),
-      error = function(e) {
-        FALSE
-      }
-    )
   } else {
     access_repo <- TRUE
   }
@@ -46,7 +51,12 @@ outdated_pkgs <- function(type = c("binary", "source")) {
   outdated_pkg_mat <- utils::old.packages(type = type, lib.loc = .libPaths()[1])
 
   if (rlang::has_length(outdated_pkg_mat) && !is.null(getOption("reuseme.ignore_update"))) {
-    indices_to_discard <- which(rownames(outdated_pkg_mat) %in% getOption("reuseme.ignore_update"))
+    if (type == "source") {
+      # only disallow update when building from source.
+      indices_to_discard <- which(rownames(outdated_pkg_mat) %in% getOption("reuseme.ignore_update"))
+    } else {
+      indices_to_discard <- integer(0L)
+    }
     if (rlang::has_length(indices_to_discard)) { # because matrix[-character(0), ] destroys |>  the matrix?
       outdated_pkg_mat <- outdated_pkg_mat[-indices_to_discard, , drop = FALSE]
     }

R/outline-criteria.R

@@ -264,7 +264,7 @@ define_outline_criteria <- function(.data, exclude_todos) {
     is_object_title = FALSE,
     tag = NA_character_,
     topic = NA_character_,
-    is_cross_ref = stringr::str_detect(content, "docs_links?\\(.") & !stringr::str_detect(content, "@param|\\{\\."),
+    is_cross_ref = stringr::str_detect(content, "docs_(links|add.+)?\\(.") & !stringr::str_detect(content, "@param|\\{\\."),
     is_function_def = grepl("<- function(", content, fixed = TRUE) & !stringr::str_starts(content, "\\s*#"),
     is_tab_or_plot_title = o_is_tab_plot_title(content) & !is_section_title & !is_function_def,
   )

R/outline.R

@@ -744,14 +744,14 @@ display_outline_element <- function(.data) {
   y <- dplyr::mutate(
     x,
     has_title_el =
-      ((line == 1 & !is_todo_fixme & !is_test_name & !is_snap_file) |
+      ((line == 1 & !is_todo_fixme & !is_test_name & !is_snap_file & !is_cross_ref) |
         (is_doc_title & !is_subtitle & !is_snap_file & !is_second_level_heading_or_more)) & !is_news,
     .by = "file"
   )
   y <- withCallingHandlers(
     dplyr::mutate(y,
       title_el_line = ifelse(has_title_el, line[
-        (line == 1 & !is_todo_fixme & !is_test_name & !is_snap_file) |
+        (line == 1 & !is_todo_fixme & !is_test_name & !is_snap_file & !is_cross_ref) |
           (is_doc_title & !is_subtitle & !is_snap_file & !is_second_level_heading_or_more)
       ][1], # take  the first element to avoid problems (may be the reason why problems occur)
       NA_integer_

R/rename.R

@@ -90,7 +90,7 @@ rename_files2 <- function(old,
   # Warn if some related files are found. If I have file.R and file.csv,
   # this will warn if I rename file.R, but not file.csv
   related_files <- fs::dir_ls(regexp = paste0(basename_remove_ext(old), "\\."), recurse = TRUE)
-  related_files <- fs::path_filter(related_files, "_snaps/|_book/|_files|_freeze|renv/", invert = TRUE)
+  related_files <- fs::path_filter(related_files, "_snaps/|_book/|_files|_freeze|renv/|\\~\\$", invert = TRUE)
   related_files <- setdiff(related_files, old)
 
   # remove project name from conflicts.

R/todo.R

@@ -7,7 +7,11 @@
 #' use `usethis::use_git_ignore("TODO.R")` if you don't want your `TODO.R` file
 #'
 #' to be included in git. If using in a package directory, use
-#' `usethis::use_build_ignore("TODO.R")` to prevent a note in `R CMD CHECK`
+#' `usethis::use_build_ignore("TODO.R")` to prevent a note in `R CMD CHECK`.
+#'
+#' If you want to write to a global TODO, use
+#'
+#' `options(reuseme.global_todo = fs::path("Documents"))` to write there.
 #'
 #' @param todo A character vector of lines to add to the TODO file. See details
 #'   for special handling.
@@ -219,7 +223,13 @@ compute_path_todo <- function(todo, proj) {
 
   # Handle special global and all syntax for todo items.
   if (proj %in% c("global", "all")) {
-    proj_path <- Sys.getenv("R_USER", Sys.getenv("HOME")) # ?base::path.expand
+    proj_path <- getOption("reuseme.global_todo")
+    if (is.null(proj_path)) {
+      cli::cli_abort(c(
+        "You must set a global option reuseme.global_todo to write to a global todo.",
+        i ="A good option for cross-platform is `options(reuseme.global_todo = fs::path_home(\"Documents\"))"
+      ))
+    }
   } else if (!is_active_proj) {
     # in interactive session with options set
     proj_path <- proj_list(proj)

README.Rmd

@@ -20,8 +20,7 @@ knitr::opts_chunk$set(
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN status](https://www.r-pkg.org/badges/version/reuseme)](https://CRAN.R-project.org/package=reuseme)
 [![R-CMD-check](https://github.com/olivroy/reuseme/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/olivroy/reuseme/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/olivroy/reuseme/branch/main/graph/badge.svg)](https://app.codecov.io/gh/olivroy/reuseme?branch=main)
-
+[![Codecov test coverage](https://codecov.io/gh/olivroy/reuseme/graph/badge.svg)](https://app.codecov.io/gh/olivroy/reuseme)
 <!-- badges: end -->
 
 The goal of reuseme is to provide utility functions for project management across RStudio projects.

README.md

@@ -11,8 +11,7 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 status](https://www.r-pkg.org/badges/version/reuseme)](https://CRAN.R-project.org/package=reuseme)
 [![R-CMD-check](https://github.com/olivroy/reuseme/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/olivroy/reuseme/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/olivroy/reuseme/branch/main/graph/badge.svg)](https://app.codecov.io/gh/olivroy/reuseme?branch=main)
-
+coverage](https://codecov.io/gh/olivroy/reuseme/graph/badge.svg)](https://app.codecov.io/gh/olivroy/reuseme)
 <!-- badges: end -->
 
 The goal of reuseme is to provide utility functions for project
@@ -210,6 +209,7 @@ outline
 #> 
 #> ── `R/files-conflicts.R`
 #> `i` TODO insert in either proj_outline, or rename_file
+#> `i` FIXME in Rbuilignore, change `^_pkgdown\.yml$` to `_pkgdown.yml` to make sure it works
 #> `i` TODO probably needs a `detect_genuine_path()`
 #> `i` Helpers
 #> `i` TODO Add false positive references
@@ -254,6 +254,7 @@ outline
 #> `i` Print interactive outline of file sections [outline]
 #> `i` `file_outline()`
 #> `i` File outline
+#> `i` TODO expand this to apply to most generated files
 #> `i` Print method
 #> `i` TODO since April 2024, cli links work almost out of the box in VScode? microsoft/vscode#176812 (<https://github.com/microsoft/vscode/issues/176812>)
 #> `i` Step: tweak outline look as they show
@@ -550,6 +551,38 @@ outline
 #> ── `tests/testthat/test-todo.R`
 #> `i` Marking TODO as done detects tags
 #> 
+#> ── `TODO.R`
+#> `i` TODO screenshot make the behaviour different when vignettes vs articles: vignettes should place it in man/figures, while articles could put it in vignettes/articles file.
+#> `i` TODO screenshot RStudio addin to insert the code directly in the qmd doc. No longer needed with RStudio 2023.12
+#> `i` TODO use_family() to edit .R file to add @family data frames tags to roxygen
+#> `i` TODO mutate_identity redundant if the focus pillar PR was merged. r-lib/pillar#585 (<https://github.com/r-lib/pillar/issues/585>)
+#> `i` TODO rename if many matches, separate those with the exact path.
+#> `i` TODO outline make ggtitle work
+#> `i` TODO outline show extra msg only for some, but in file outline, not in proj?
+#> `i` TODO outline detect help calls and apply markup. `?fs::file_show` disregard finishing `.` (not followed by dot)
+#> `i` TODO outline renable cli info.
+#> `i` TODO escape_markup doesn't work with complex operation {x^2} for example. Maybe if detecting something complex, use cli_escape function. escape-complex-markyp branch created to try to address this.
+#> `i` TODO outline avoid evaluating in current env.
+#> `i` TODO wrap regexps in functions
+#> `i` TODO outline remove examples from outline. Sometimes commented code is caught.
+#> `i` TODO outline roxygen comments processing should be left to `roxygen2::parse_file()`
+#> `i` TODO outline show key like `pak::pkg_deps_tree()` does.
+#> `i` TODO outline roxygen function title
+#> `i` TODO outline remove ggtext markup from plot title.
+#> `i` FIXME outline comments are now interpreted as section
+#> `i` TODO outline todos in qmd file inside html comment
+#> `i` TODO reframe more than one issue. nw drive
+#> `i` TODO delete generated files
+#> `i` TODO [check_referenced_files] doesn't check for 'R/file.R'
+#> `i` TODO browse_pkg should open by default if no vignettes are found, because there is not much to do in the R-session.
+#> `i` TODO exclude _files from `proj_list()`
+#> `i` TODO rename_files should be less noisy about project name file
+#> `i` TODO add_to_tricks(). when detecting TRICK like complete todo, but not remove line. requires a scheme. moves the item to tricks.md at the correct place. (copy to clipboard is probably enough)
+#> `i` TODO use vapply() instead of purrr::map
+#> `i` TODO rename_files() should know about .covrignore too
+#> `i` TODO withr::local_dir for proj_outline.
+#> `i` TODO add warn_conflicts = 'none'
+#> 
 #> ── `NEWS.md`
 #> `i` reuseme (development version)
 #> 

TODO.R

@@ -30,3 +30,7 @@
 # TODO [outline] family should be displayed differently..
 # TODO [outline] find a way to make print bookmarks..
 # TODO [outline] escape some content in headings see {.file tests/testthat/_outline/quarto-caps.md} for examples.
+# TODO use vapply() instead of purrr::map
+# TODO rename_files() should know about .covrignore too
+# TODO withr::local_dir for proj_outline.
+# TODO add warn_conflicts = 'none'