Merge branch 'main' into xml-utils

.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

@@ -34,10 +34,9 @@ jobs:
  # use 4.1 to check with rtools40's older compiler
  - {os: windows-latest, r: '4.1'}
 
- # 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'}
@@ -72,7 +71,6 @@ jobs:
  http-user-agent: ${{ matrix.config.http-user-agent }}
  use-public-rspm: true
 
- # `{patrick}` imports `{purrr}`, and so needs to be ignored on R < 3.5
  - uses: r-lib/actions/setup-r-dependencies@v2
  with:
  extra-packages: |

.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

@@ -1,45 +1,38 @@
-linters: linters_with_defaults(
- any_duplicated_linter(),
- any_is_na_linter(),
- backport_linter("oldrel-4", except = c("R_user_dir", "str2lang", "str2expression", "deparse1", "...names")),
- consecutive_assertion_linter(),
- expect_comparison_linter(),
- expect_identical_linter(),
- expect_length_linter(),
- expect_named_linter(),
- expect_not_linter(),
- expect_null_linter(),
- expect_s3_class_linter(),
- expect_s4_class_linter(),
- expect_true_false_linter(),
- expect_type_linter(),
- fixed_regex_linter(),
- for_loop_index_linter(),
- if_not_else_linter(),
- implicit_assignment_linter(),
- implicit_integer_linter(),
- keyword_quote_linter(),
- lengths_linter(),
- line_length_linter(120),
- missing_argument_linter(),
- nested_ifelse_linter(),
- numeric_leading_zero_linter(),
- outer_negation_linter(),
- paste_linter(),
- redundant_equals_linter(),
- redundant_ifelse_linter(),
- sort_linter(),
- sprintf_linter(),
- strings_as_factors_linter(),
- undesirable_function_linter(c(Sys.setenv = NA_character_, mapply = NA_character_, structure = NA_character_)),
- unnecessary_nested_if_linter(),
- unnecessary_lambda_linter(),
+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,
+ options = NULL
+ )),
+ undesirable_operator_linter(modify_defaults(
+ defaults = default_undesirable_operators,
+ `:::` = NULL,
+ `<<-` = NULL
+ )),
  unnecessary_concatenation_linter(allow_single_expression = FALSE),
- yoda_test_linter()
+ absolute_path_linter = NULL,
+ library_call_linter = NULL,
+ nonportable_path_linter = NULL,
+ todo_comment_linter = NULL,
+ # TODO(#2327): Enable this.
+ unreachable_code_linter = NULL
  )
 exclusions: list(
  "inst/doc/creating_linters.R" = 1,
  "inst/example/bad.R",
+ "tests/testthat.R" = list(unused_import_linter = Inf),
  "tests/testthat/default_linter_testcode.R",
  "tests/testthat/dummy_packages",
  "tests/testthat/dummy_projects",

COPYING

@@ -1,4 +1,4 @@
-Copyright (c) 2014-2022, James Hester
+Copyright (c) 2014-2024, James Hester
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the