Merge branch 'main' into check-random-order

.Rbuildignore

@@ -8,6 +8,7 @@
 ^\.Rproj\.user$
 ^\.idea$
 ^\.dev$
+^\.devcontainer$
 ^\.lintr$
 ^\.lintr_new$
 ^wercker\.yml$

.dev/lint_metadata_test.R

@@ -0,0 +1,54 @@
+# This script is designed to find linters that lack metadata tests.
+#   To do so, it forces Lint() to give the wrong information,
+#   runs the test suite, and finds linters that nevertheless pass all their tests.
+library(testthat)
+
+lint_file <- "R/lint.R"
+
+original <- readLines(lint_file)
+expected_line <- "line_number = as.integer(line_number)"
+if (sum(grepl(expected_line, original, fixed = TRUE)) != 1L) {
+  stop(sprintf(
+    "Please update this workflow -- need exactly one hit for line '%s' in file '%s'.",
+    expected_line, lint_file
+  ))
+}
+writeLines(
+  sub(expected_line, "line_number = as.integer(2^31 - 1)", original, fixed = TRUE),
+  lint_file
+)
+# Not useful in CI but good when running locally.
+withr::defer({
+  writeLines(original, lint_file)
+  pkgload::load_all()
+})
+
+pkgload::load_all()
+
+report <- test_dir(
+  "tests/testthat",
+  filter = "linter$",
+  stop_on_failure = FALSE,
+  reporter = SilentReporter$new()
+)
+names(report) <- gsub("^test-|\\.R$", "", vapply(report, `[[`, "file", FUN.VALUE = character(1L)))
+
+# Hack the nested structure of the testthat report to identify which files have
+#   any failed test
+failed <- report |>
+  vapply(
+    \(x) any(vapply(x$results, inherits, "expectation_failure", FUN.VALUE = logical(1L))),
+    logical(1L)
+  ) |>
+  which() |>
+  names() |>
+  unique()
+
+passed <- setdiff(
+  available_linters(tags = NULL)$linter,
+  failed
+)
+
+if (length(passed) > 0L) {
+  stop("Please add tests of lint metadata for the following linters: ", toString(passed))
+}

.dev/roxygen_test.R

@@ -0,0 +1,54 @@
+# Test to ensure roxygenize() has been run on the current PR
+library(tools)
+library(roxygen2)
+
+old_dir <- file.path(tempdir(), "man")
+if (dir.exists(old_dir)) unlink(old_dir, recursive = TRUE)
+file.copy("man", tempdir(), recursive = TRUE)
+old_files <- list.files(old_dir, pattern = "\\.Rd$")
+new_dir <- "man"
+.Last <- function() unlink(old_dir, recursive = TRUE)
+
+# Rd2txt() prints to its out= argument, so we'd have to compare file contents;
+#   plain parse_Rd() keeps srcref info that encodes the file path, which as.character() strips.
+normalize_rd <- function(rd_file) as.character(parse_Rd(rd_file))
+
+rd_equal <- function(f1, f2) isTRUE(all.equal(normalize_rd(f1), normalize_rd(f2)))
+
+check_roxygenize_idempotent <- function(LOCALE) {
+  Sys.setlocale("LC_COLLATE", LOCALE)
+  roxygenize()
+
+  new_files <- list.files(new_dir, pattern = "\\.Rd$")
+
+  old_not_new <- setdiff(old_files, new_files)
+  if (length(old_not_new) > 0L) {
+    stop("Found saved .Rd files gone from a fresh run of roxygenize(): ", toString(old_not_new))
+  }
+
+  new_not_old <- setdiff(new_files, old_files)
+  if (length(new_not_old) > 0L) {
+    stop("Found new .Rd files from a fresh run of roxygenize(): ", toString(new_not_old))
+  }
+
+  for (file in new_files) {
+    old_file <- file.path(old_dir, file)
+    new_file <- file.path(new_dir, file)
+    if (rd_equal(old_file, new_file)) {
+      next
+    }
+    cat(sprintf("roxygenize() output differs from saved output for %s.\n", file))
+    cat("Here's the 'diff' comparison of the two files:\n")
+    cat("  [---]: saved output in man/ directory\n")
+    cat("  [+++]: roxygenize() output of R/ sources\n")
+    system2("diff", c("--unified", old_file, new_file))
+    stop("Failed in LOCALE=", LOCALE, ".", call. = FALSE)
+  }
+}
+
+# Run the check in a few locales to ensure there's no idempotency issues w.r.t. sorting, too
+for (LOCALE in c("C", "en_US", "hu_HU", "ja_JP")) {
+  check_roxygenize_idempotent(LOCALE)
+}
+
+unlink(old_dir, recursive = TRUE)

.devcontainer/Dockerfile

@@ -0,0 +1,14 @@
+FROM rocker/r-base
+
+RUN apt-get -qq update && \
+  apt-get install -y --no-install-recommends git libxml2-dev
+
+COPY DESCRIPTION .
+
+RUN Rscript -e '                           \
+  install.packages("remotes");             \
+  remotes::install_deps(dependencies = c(  \
+    "Imports",                             \
+    "Config/needs/development"             \
+  ))                                       \
+'

.devcontainer/devcontainer.json

@@ -0,0 +1,3 @@
+{
+    "build": { "dockerfile": "Dockerfile", "context": ".."}
+}

.github/CODE_OF_CONDUCT.md

@@ -59,7 +59,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at james.f.hester@gmail.com. 
+reported to the community leaders responsible for enforcement at michaelchirico4@gmail.com. 
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

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

@@ -37,7 +37,7 @@ jobs:
           # Use older ubuntu to maximise backward compatibility
           - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release', locale: 'en_US'}
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release', locale: 'zh_CN'}
+          - {os: ubuntu-latest,  r: 'release', http-user-agent: 'release', locale: 'zh_CN'}
           - {os: ubuntu-latest,  r: 'release'}
           - {os: ubuntu-latest,  r: 'oldrel-1'}
           - {os: ubuntu-latest,  r: 'oldrel-2'}

.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@v4.4.3
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/repo-meta-tests.yaml

@@ -0,0 +1,38 @@
+# Various repo-level tests for code quality
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: repo-meta-tests
+
+jobs:
+  repo-meta-tests:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "release"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::roxygen2
+
+      - name: Ensure lint metadata is tested
+        run: |
+          options(crayon.enabled = TRUE)
+          callr::rscript(".dev/lint_metadata_test.R")
+        shell: Rscript {0}
+
+      - name: Ensure roxygen content matches man directory
+        run: |
+          callr::rscript(".dev/roxygen_test.R")
+        shell: Rscript {0}

.lintr

@@ -2,6 +2,15 @@ linters: all_linters(
     backport_linter("3.6.0", except = c("R_user_dir", "deparse1", "...names")),
     line_length_linter(120L),
     object_overwrite_linter(allow_names = c("line", "lines", "pipe", "symbols")),
+    todo_comment_linter(
+      except_regex = rex::rex(
+        "TODO(",
+        # GitHub issue number #1234, possibly from another repo org/repo#5678
+        maybe(one_or_more(character_class("a-zA-Z0-9-")), "/", one_or_more(character_class("a-zA-Z0-9._-"))),
+        "#", one_or_more(digit),
+        ")"
+      )
+    ),
     undesirable_function_linter(modify_defaults(
       defaults = default_undesirable_functions,
       library = NULL,
@@ -14,7 +23,6 @@ linters: all_linters(
     )),
     unnecessary_concatenation_linter(allow_single_expression = FALSE),
     absolute_path_linter = NULL,
-    extraction_operator_linter = NULL,
     library_call_linter = NULL,
     nonportable_path_linter = NULL,
     todo_comment_linter = NULL,

DESCRIPTION

@@ -2,11 +2,11 @@ Package: lintr
 Title: A 'Linter' for R Code
 Version: 3.1.1.9000
 Authors@R: c(
-    person("Jim", "Hester", , "[email protected]", role = c("aut", "cre")),
+    person("Jim", "Hester", , role = "aut"),
     person("Florent", "Angly", role = "aut",
            comment = "fangly"),
     person("Russ", "Hyde", role = "aut"),
-    person("Michael", "Chirico", role = "aut"),
+    person("Michael", "Chirico", email = "[email protected]", role = c("aut", "cre")),
     person("Kun", "Ren", role = "aut"),
     person("Alexander", "Rosenstock", role = "aut",
            comment = "AshesITR"),
@@ -37,14 +37,12 @@ Imports:
 Suggests:
     bookdown,
     cli,
-    httr (>= 1.2.1),
     jsonlite,
-    mockery,
-    patrick,
+    patrick (>= 0.2.0),
     rlang,
     rmarkdown,
     rstudioapi (>= 0.2),
-    testthat (>= 3.1.5),
+    testthat (>= 3.2.1),
     tibble,
     tufte,
     withr (>= 2.5.0)
@@ -53,10 +51,11 @@ Enhances:
 VignetteBuilder: 
     knitr
 Config/Needs/website: tidyverse/tidytemplate
+Config/Needs/development: pkgload, cli, testthat, patrick
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate:
     'make_linter_from_xpath.R'
     'xp_utils.R'
@@ -75,8 +74,7 @@ Collate:
     'cache.R'
     'class_equals_linter.R'
     'commas_linter.R'
-    'comment_linters.R'
-    'comments.R'
+    'commented_code_linter.R'
     'comparison_negation_linter.R'
     'condition_call_linter.R'
     'condition_message_linter.R'
@@ -102,7 +100,6 @@ Collate:
     'expect_true_false_linter.R'
     'expect_type_linter.R'
     'extract.R'
-    'extraction_operator_linter.R'
     'fixed_regex_linter.R'
     'for_loop_index_linter.R'
     'function_argument_linter.R'
@@ -143,6 +140,7 @@ Collate:
     'nested_ifelse_linter.R'
     'nested_pipe_linter.R'
     'nonportable_path_linter.R'
+    'shared_constants.R'
     'nrow_subset_linter.R'
     'numeric_leading_zero_linter.R'
     'nzchar_linter.R'
@@ -175,8 +173,8 @@ Collate:
     'seq_linter.R'
     'settings.R'
     'settings_utils.R'
-    'shared_constants.R'
     'sort_linter.R'
+    'source_utils.R'
     'spaces_inside_linter.R'
     'spaces_left_parentheses_linter.R'
     'sprintf_linter.R'
@@ -185,14 +183,14 @@ Collate:
     'strings_as_factors_linter.R'
     'system_file_linter.R'
     'terminal_close_linter.R'
+    'todo_comment_linter.R'
     'trailing_blank_lines_linter.R'
     'trailing_whitespace_linter.R'
     'tree_utils.R'
     'undesirable_function_linter.R'
     'undesirable_operator_linter.R'
     'unnecessary_concatenation_linter.R'
     'unnecessary_lambda_linter.R'
-    'unnecessary_nested_if_linter.R'
     'unnecessary_nesting_linter.R'
     'unnecessary_placeholder_linter.R'
     'unreachable_code_linter.R'

NAMESPACE

@@ -95,6 +95,7 @@ export(linters_with_defaults)
 export(linters_with_tags)
 export(list_comparison_linter)
 export(literal_coercion_linter)
+export(make_linter_from_function_xpath)
 export(make_linter_from_xpath)
 export(matrix_apply_linter)
 export(missing_argument_linter)
@@ -190,6 +191,7 @@ importFrom(utils,tail)
 importFrom(utils,txtProgressBar)
 importFrom(xml2,as_list)
 importFrom(xml2,xml_attr)
+importFrom(xml2,xml_children)
 importFrom(xml2,xml_find_all)
 importFrom(xml2,xml_find_chr)
 importFrom(xml2,xml_find_first)