Merge branch 'main' into f2599-cli-progress-bar

.Rbuildignore

@@ -23,9 +23,11 @@
 ^bench$
 ^tests/testthat/dummy_packages/package/[.]Rbuildignore$
 ^tests/testthat/dummy_packages/cp1252/[.]Rbuildignore$
+testthat-problems[.]rds$
 ^_pkgdown\.yaml$
 ^docs$
 ^pkgdown$
 ^vignettes/[^-]+.gif$
 ^CRAN-SUBMISSION$
 ^CODE_OF_CONDUCT\.md$
+^paper$

.github/workflows/draft-pdf.yml

@@ -0,0 +1,30 @@
+# TODO: delete this file once the paper is published
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.github/workflows/pkgdown.yaml

@@ -39,7 +39,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.6.3
+        uses: JamesIves/github-pages-deploy-action@v4.7.1
         with:
           clean: false
           branch: gh-pages

NEWS.md

@@ -18,6 +18,8 @@
 * `cyclocomp_linter()` is no longer part of the default linters (#2555, @IndrajeetPatil) because the tidyverse style guide doesn't contain any guidelines on meeting certain complexity requirements. Note that users with `cyclocomp_linter()` in their configs may now need to install {cyclocomp} intentionally, in particular in CI/CD pipelines.
 * `scalar_in_linter` is now configurable to allow other `%in%` like operators to be linted. The data.table operator `%chin%` is no longer linted by default; use `in_operators = "%chin%"` to continue linting it. (@F-Noelle)
 * `lint()` and friends now normalize paths to forward slashes on Windows (@olivroy, #2613).
+* `undesirable_function_linter()`, `undesirable_operator_linter()`, and `list_comparison_linter()` were removed from the tag `efficiency` (@IndrajeetPatil, #2655). If you use `linters_with_tags("efficiency")` to include these linters, you'll need to adjust your config to keep linting your code against them. We did not find any such users on GitHub.
+
 
 ## Bug fixes
 
@@ -27,6 +29,7 @@
 * `.lintr` configs set by option `lintr.linter_file` or environment variable `R_LINTR_LINTER_FILE` can point to subdirectories (#2512, @MichaelChirico).
 * `indentation_linter()` returns `ranges[1L]==1L` when the offending line has 0 spaces (#2550, @MichaelChirico).
 * `literal_coercion_linter()` doesn't surface a warning about NAs during coercion for code like `as.integer("a")` (#2566, @MichaelChirico).
+* `commented_code_linter()` can detect commented code that ends with a pipe (#2671, @jcken95)
 
 ## Changes to default linters
 
@@ -84,10 +87,13 @@
 ### Lint accuracy fixes: removing false positives
 
 * `object_name_linter()` and `object_length_linter()` ignore {rlang} name injection like `x |> mutate("{new_name}" := foo(col))` (#1926, @MichaelChirico). No checking is applied in such cases. {data.table} in-place assignments like `DT[, "sPoNGeBob" := "friend"]` are still eligible for lints.
+* `object_usage_linter()` finds global variables assigned with `=` or `->`, which avoids some issues around "undefined global variables" in scripts (#2654, @MichaelChirico).
 
 ## Notes
 
 * All user-facing messages (including progress bar) are now prepared using the `{cli}` package (#2418 and #2641, @IndrajeetPatil). All messages have been reviewed and updated to be more informative and consistent.
+* All user-facing messages are now prepared using the `{cli}` package (#2418, @IndrajeetPatil). All messages have been reviewed and updated to be more informative and consistent.
+* File locations in lints and error messages contain clickable hyperlinks to improve code navigation (#2645, #2588, @olivroy).
 * {lintr} now depends on R version 4.0.0. It already does so implicitly due to recursive upstream dependencies requiring this version; we've simply made that dependency explicit and up-front (#2569, @MichaelChirico).
 
 # lintr 3.1.2

R/class_equals_linter.R

@@ -48,9 +48,10 @@ class_equals_linter <- function() {
     bad_expr <- xml_find_all(xml_calls, xpath)
 
     operator <- xml_find_chr(bad_expr, "string(*[2])")
-    lint_message <- sprintf(
-      "Use inherits(x, 'class-name'), is.<class> or is(x, 'class') instead of comparing class(x) with %s.",
-      operator
+    lint_message <- paste0(
+      "Use inherits(x, 'class-name'), is.<class> for S3 classes, ",
+      "or is(x, 'S4Class') for S4 classes, ",
+      "instead of comparing class(x) with ", operator, "."
     )
     xml_nodes_to_lints(
       bad_expr,

R/commented_code_linter.R

@@ -83,9 +83,10 @@ commented_code_linter <- function() {
     all_comments <- xml_text(all_comment_nodes)
     code_candidates <- re_matches(all_comments, code_candidate_regex, global = FALSE, locations = TRUE)
     extracted_code <- code_candidates[, "code"]
-    # ignore trailing ',' when testing for parsability
-    extracted_code <- re_substitutes(extracted_code, rex(",", any_spaces, end), "")
+    # ignore trailing ',' or pipes ('|>', '%>%') when testing for parsability
+    extracted_code <- re_substitutes(extracted_code, rex(or(",", "|>", "%>%"), any_spaces, end), "")
     extracted_code <- re_substitutes(extracted_code, rex(start, any_spaces, ","), "")
+
     is_parsable <- which(vapply(extracted_code, parsable, logical(1L)))
 
     lint_list <- xml_nodes_to_lints(

R/extract.R

@@ -9,7 +9,7 @@ extract_r_source <- function(filename, lines, error = identity) {
   output <- rep.int(NA_character_, length(lines))
 
   chunks <- tryCatch(get_chunk_positions(pattern = pattern, lines = lines), error = error)
-  if (inherits(chunks, "error") || inherits(chunks, "lint")) {
+  if (is_error(chunks) || is_lint(chunks)) {
     assign("e", chunks, envir = parent.frame())
     # error, so return empty code
     return(output)

R/get_source_expressions.R

@@ -86,7 +86,7 @@ get_source_expressions <- function(filename, lines = NULL) {
   source_expression$content <- get_content(source_expression$lines)
   parsed_content <- get_source_expression(source_expression, error = function(e) lint_parse_error(e, source_expression))
 
-  if (inherits(e, "lint") && (is.na(e$line) || !nzchar(e$line) || e$message == "unexpected end of input")) {
+  if (is_lint(e) && (is.na(e$line) || !nzchar(e$line) || e$message == "unexpected end of input")) {
     # Don't create expression list if it's unreliable (invalid encoding or unhandled parse error)
     expressions <- list()
   } else {
@@ -502,7 +502,7 @@ get_source_expression <- function(source_expression, error = identity) {
     error = error
   )
 
-  if (inherits(parsed_content, c("error", "lint"))) {
+  if (is_error(parsed_content) || is_lint(parsed_content)) {
     assign("e", parsed_content, envir = parent.frame())
     parse_error <- TRUE
   }
@@ -513,7 +513,7 @@ get_source_expression <- function(source_expression, error = identity) {
     error = error
   )
 
-  if (inherits(parsed_content, c("error", "lint"))) {
+  if (is_error(parsed_content) || is_lint(parsed_content)) {
     # Let parse errors take precedence over encoding problems
     if (!parse_error) assign("e", parsed_content, envir = parent.frame())
     return() # parsed_content is unreliable if encoding is invalid

R/lint.R

@@ -680,7 +680,7 @@ has_positional_logical <- function(dots) {
 }
 
 maybe_append_error_lint <- function(lints, error, lint_cache, filename) {
-  if (inherits(error, "lint")) {
+  if (is_lint(error)) {
     error$linter <- "error"
     lints[[length(lints) + 1L]] <- error
 

R/methods.R

@@ -1,27 +1,16 @@
 #' @export
 format.lint <- function(x, ..., width = getOption("lintr.format_width")) {
-  if (requireNamespace("cli", quietly = TRUE)) {
-    color <- switch(x$type,
-      warning = cli::col_magenta,
-      error = cli::col_red,
-      style = cli::col_blue,
-      cli::style_bold
-    )
-    emph <- cli::style_bold
-  } else {
-    # nocov start
-    color <- identity
-    emph <- identity
-    # nocov end
-  }
+  color <- switch(x$type,
+    warning = cli::col_magenta,
+    error = cli::col_red,
+    style = cli::col_blue,
+    cli::style_bold
+  )
+  emph <- cli::style_bold
 
+  line_ref <- build_line_ref(x)
   annotated_msg <- paste0(
-    emph(
-      x$filename, ":",
-      as.character(x$line_number), ":",
-      as.character(x$column_number), ": ",
-      sep = ""
-    ),
+    emph(line_ref, ": "),
     color(x$type, ": ", sep = ""),
     "[", x$linter, "] ",
     emph(x$message)
@@ -40,6 +29,19 @@ format.lint <- function(x, ..., width = getOption("lintr.format_width")) {
   )
 }
 
+build_line_ref <- function(x) {
+  line_ref <- paste0(
+    x$filename, ":",
+    as.character(x$line_number), ":",
+    as.character(x$column_number)
+  )
+
+  if (!cli::ansi_has_hyperlink_support()) {
+    return(line_ref)
+  }
+  cli::format_inline("{.path {line_ref}}")
+}
+
 #' @export
 print.lint <- function(x, ...) {
   cat(format(x, ...))

R/object_usage_linter.R

@@ -148,8 +148,10 @@ get_assignment_symbols <- function(xml) {
   get_r_string(xml_find_all(
     xml,
     "
-      expr[LEFT_ASSIGN]/expr[1]/SYMBOL[1] |
+      expr[LEFT_ASSIGN or EQ_ASSIGN]/expr[1]/SYMBOL[1] |
+      expr[RIGHT_ASSIGN]/expr[2]/SYMBOL[1] |
       equal_assign/expr[1]/SYMBOL[1] |
+      expr_or_assign_or_help/expr[1]/SYMBOL[1] |
       expr[expr[1][SYMBOL_FUNCTION_CALL/text()='assign']]/expr[2]/* |
       expr[expr[1][SYMBOL_FUNCTION_CALL/text()='setMethod']]/expr[2]/*
     "

R/redundant_equals_linter.R

@@ -19,6 +19,11 @@
 #'   linters = redundant_equals_linter()
 #' )
 #'
+#' lint(
+#'   text = "dt[is_tall == FALSE, y]",
+#'   linters = redundant_equals_linter()
+#' )
+#'
 #' # okay
 #' lint(
 #'   text = "if (any(x)) 1",
@@ -30,6 +35,12 @@
 #'   linters = redundant_equals_linter()
 #' )
 #'
+#' # in `{data.table}` semantics, `dt[x]` is a join, `dt[(x)]` is a subset
+#' lint(
+#'   text = "dt[(!is_tall), y]",
+#'   linters = redundant_equals_linter()
+#' )
+#'
 #' @evalRd rd_tags("redundant_equals_linter")
 #' @seealso
 #' - [linters] for a complete list of linters available in lintr.

R/seq_linter.R

@@ -7,7 +7,8 @@
 #' Additionally, it checks for `1:n()` (from `{dplyr}`) and `1:.N` (from `{data.table}`).
 #'
 #' These often cause bugs when the right-hand side is zero.
-#' It is safer to use [base::seq_len()] or [base::seq_along()] instead.
+#' Instead, it is safer to use [base::seq_len()] (to create a sequence of a specified *length*) or
+#'   [base::seq_along()] (to create a sequence *along* an object).
 #'
 #' @examples
 #' # will produce lints

R/utils.R

@@ -245,9 +245,12 @@ get_r_string <- function(s, xpath = NULL) {
 }
 
 is_linter <- function(x) inherits(x, "linter")
+is_lint <- function(x) inherits(x, "lint")
+
+is_error <- function(x) inherits(x, "error")
 
 is_tainted <- function(lines) {
-  inherits(tryCatch(nchar(lines), error = identity), "error")
+  is_error(tryCatch(nchar(lines), error = identity))
 }
 
 #' Check that the entries in ... are valid

inst/lintr/linters.csv

@@ -52,7 +52,7 @@ length_test_linter,common_mistakes efficiency
 lengths_linter,efficiency readability best_practices
 library_call_linter,style best_practices readability configurable
 line_length_linter,style readability default configurable
-list_comparison_linter,best_practices common_mistakes efficiency
+list_comparison_linter,best_practices common_mistakes
 literal_coercion_linter,best_practices consistency efficiency
 matrix_apply_linter,readability efficiency
 missing_argument_linter,correctness common_mistakes configurable
@@ -108,8 +108,8 @@ terminal_close_linter,best_practices robustness
 todo_comment_linter,style configurable
 trailing_blank_lines_linter,style default
 trailing_whitespace_linter,style default configurable
-undesirable_function_linter,style efficiency configurable robustness best_practices
-undesirable_operator_linter,style efficiency configurable robustness best_practices
+undesirable_function_linter,style configurable robustness best_practices
+undesirable_operator_linter,style configurable robustness best_practices
 unnecessary_concatenation_linter,style readability efficiency configurable
 unnecessary_lambda_linter,best_practices efficiency readability configurable
 unnecessary_nested_if_linter,readability best_practices deprecated

paper/.gitignore

@@ -0,0 +1 @@
+/.quarto/