chore: Formatting and linting

Author: csgillespie

.lintr

@@ -1,6 +1,5 @@
-linters: with_defaults(
+linters: lintr::linters_with_defaults(
     assignment_linter = NULL,
     commented_code_linter = NULL,
-    line_length_linter(100),
-    cyclocomp_linter = NULL
-    )
+    line_length_linter = lintr::line_length_linter(100)
+  )

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: inteRgrate
 Title: Opinionated Package Coding Styles
-Version: 1.0.22
+Version: 1.0.23
 Authors@R:
     person("Jumping", "Rivers", , "info@jumpingrivers.com", role = c("aut", "cre"))
 Description: A set of functions to enforce styling in functions.  This
@@ -18,9 +18,10 @@ Imports:
     tibble,
     usethis
 Suggests:
+    cyclocomp,
     roxygen2,
     testthat,
     withr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,3 +1,6 @@
+# inteRgrate 1.0.23 (2026-01-22)
+  * chore: Spring clean; formatting linting, running jarl
+
 # inteRgrate 1.0.22 _2022-05-25_
   * Bug: Remove empty lines from .Rbuildignore for `check_version()`
 
@@ -38,10 +41,10 @@
 # inteRgrate 1.0.8 _2021-01-05_
   * Feature: `check_version()` now works with multiple pkgs in a repo
   * Bug: `check_lintr()` ignores `R/*.rda` files (fixes #33)
-  
+
 # inteRgrate 1.0.7 _2020-11-25_
   * Feature: `check_all()` to run all checks
-  * Feature: Call `stop()` at the of the checks 
+  * Feature: Call `stop()` at the of the checks
 
 # inteRgrate 1.0.6 _2020-10-23_
   * Feature: allow `*` as emphasis indicator
@@ -64,7 +67,7 @@
   * Feature: Ensure files end with a line break
   * Feature: Build pkgs and set ENV variables
   * Feature: Add tests for yml parsing
-  
+
 # inteRgrate 1.0.1
   * Breaking changes
   * Feature: use __rcmdcheck__ instead of __devtools__. This breaks/changes a few things.

R/build.R

@@ -18,7 +18,7 @@ build_pkg = function() {
   set_renviron_var("PKG_TARBALL_PATH", full_path)
   cli::cli_alert_info("PKG_TARBALL_PATH {full_path}")
 
-  return(pkg_tar_ball)
+  pkg_tar_ball
 }
 
 #' @rdname build_pkg

R/check_all.R

@@ -10,13 +10,21 @@
 #' @details The arguments for the function correspond to a particular check, e.g. check_ARGNAME().
 #' Note: As this package matures, this function will include the newer checks.
 #' @export
-check_all  = function(pkg = TRUE, lintr = TRUE,
-                      namespace = TRUE, r_filenames = TRUE,
-                      version = TRUE, gitignore = TRUE,
-                      tidy_description = TRUE, readme = TRUE,
-                      file_permissions = TRUE, line_breaks = TRUE,
-                      tag = TRUE, news = TRUE,
-                      rproj = TRUE) {
+check_all = function(
+  pkg = TRUE,
+  lintr = TRUE,
+  namespace = TRUE,
+  r_filenames = TRUE,
+  version = TRUE,
+  gitignore = TRUE,
+  tidy_description = TRUE,
+  readme = TRUE,
+  file_permissions = TRUE,
+  line_breaks = TRUE,
+  tag = TRUE,
+  news = TRUE,
+  rproj = TRUE
+) {
   .check$all = TRUE
   # Extract all arguments and values
   args = as.list(environment())
@@ -30,5 +38,5 @@ check_all  = function(pkg = TRUE, lintr = TRUE,
     msg_error("Issues Detected")
     stop("Please fix")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }

R/check_gitignore.R

@@ -41,21 +41,29 @@ check_gitignore = function(path = ".") {
   ## .e.g *.synctex(busy)
   ignores = ignores[!stringr::str_detect(ignores, pattern = "\\(|\\)")]
 
-  list_ignores = sapply(glob2rx(ignores, trim.head = FALSE, trim.tail = FALSE),
-                        function(ignore) stringr::str_detect(git_global_ignore, ignore))
+  list_ignores = sapply(
+    glob2rx(ignores, trim.head = FALSE, trim.tail = FALSE),
+    function(ignore) stringr::str_detect(git_global_ignore, ignore)
+  )
 
-  mat_ignores = matrix(list_ignores, ncol = length(git_global_ignore), byrow = TRUE)
+  mat_ignores = matrix(
+    list_ignores,
+    ncol = length(git_global_ignore),
+    byrow = TRUE
+  )
 
   ignore_files = apply(mat_ignores, 2, any)
   missing_ignores = git_global_ignore[!ignore_files]
   if (length(missing_ignores) != 0L) {
     for (ignore in missing_ignores) {
       msg_error(paste("Missing", ignore, " from .gitignore"))
     }
-    msg_error("Copying github.com/github/gitignore/blob/master/R.gitignore is a good start.")
+    msg_error(
+      "Copying github.com/github/gitignore/blob/master/R.gitignore is a good start."
+    )
     msg_error("Please update your .gitignore")
   } else {
     cli::cli_alert_success(".gitignore looks good")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }

R/check_lintr.R

@@ -1,23 +1,32 @@
 get_exclusions = function() {
-  if (!file.exists(".lintr")) return(c("^R/|^cache/|^packrat/|^renv/"))
+  if (!file.exists(".lintr")) {
+    return(c("^R/|^cache/|^packrat/|^renv/"))
+  }
 
   exclusions = read.dcf(".lintr", all = TRUE)$exclusions
 
-  if (is.null(exclusions)) return(c("^R/|^cache/|^packrat/|^renv/"))
+  if (is.null(exclusions)) {
+    return(c("^R/|^cache/|^packrat/|^renv/"))
+  }
   exclusions = stringr::str_split(exclusions, ",")[[1]]
   exclusions = stringr::str_remove(exclusions, "list\\W?\\(")
   exclusions = stringr::str_remove(exclusions, "\\)$")
   exclusions = stringr::str_squish(exclusions)
   exclusions = stringr::str_remove_all(exclusions, ("^\"|\"$"))
 
   ## Convert to regular expression
-  pattern = paste0(c(exclusions, "^R/", "^cache/", "^packrat/", "^renv/"), collapse = "|")
-  return(pattern)
+  pattern = paste0(
+    c(exclusions, "^R/", "^cache/", "^packrat/", "^renv/"),
+    collapse = "|"
+  )
+  pattern
 }
 
 lint_files = function() {
   lint_errors = FALSE
-  lints = lintr::lint_package(exclusions = list("R/RcppExports.R", "renv", "packrat", "cache"))
+  lints = lintr::lint_package(
+    exclusions = list("R/RcppExports.R", "renv", "packrat", "cache")
+  )
   if (length(lints) > 0) {
     lapply(lints, print)
     lint_errors = TRUE
@@ -34,7 +43,7 @@ lint_files = function() {
     }
   }
 
-  return(lint_errors)
+  lint_errors
 }
 
 #' @title The lintr check
@@ -63,5 +72,5 @@ check_lintr = function(path = ".") {
   } else {
     cli::cli_alert_success("Lint looks good")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }

R/check_namespace.R

@@ -16,25 +16,33 @@ check_namespace = function(no_imports = NULL, path = ".") {
   cli::cli_h3("Checking namespace for imports()...check_namespace()")
   namespace = readLines(file.path(path, "NAMESPACE"))
 
-  imports_only = namespace[substr(namespace, 1, 7) == "import("]
+  imports_only = namespace[startsWith(namespace, "import(")]
   if (length(imports_only) == no_imports) {
-    msg = glue("Imports look good - {length(imports_only)} found, {no_imports} allowed")
+    msg = glue(
+      "Imports look good - {length(imports_only)} found, {no_imports} allowed"
+    )
     cli::cli_alert_success(msg)
     return(invisible(NULL))
   } else if (length(imports_only) < no_imports) {
-    msg = glue("Imports look good - {length(imports_only)} found, {no_imports} allowed.
-               But you could reduce the number of imports allowed")
+    msg = glue(
+      "Imports look good - {length(imports_only)} found, {no_imports} allowed.
+               But you could reduce the number of imports allowed"
+    )
     cli::cli_alert_warning(msg)
     return(invisible(NULL))
   }
 
   imports_only = substr(imports_only, 8, nchar(imports_only) - 1)
   for (import in imports_only) {
-    msg = glue::glue("The package {import} is being directly imported - \\
-               use importFrom instead.")
+    msg = glue::glue(
+      "The package {import} is being directly imported - \\
+               use importFrom instead."
+    )
     msg_error(msg)
   }
-  msg = glue::glue("A total of {length(imports_only)} imports detected. \\
-                   But only {no_imports} are allowed.")
+  msg = glue::glue(
+    "A total of {length(imports_only)} imports detected. \\
+                   But only {no_imports} are allowed."
+  )
   msg_error(msg)
 }

R/check_news.R

@@ -1,9 +1,14 @@
 check_news_major = function(news, pkg_name, version) {
-  pattern = glue::glue("^# <pkg_name> <version> [_\\*]20\\d{2}-\\d{2}-\\d{2}[_\\*]$",
-                       .open = "<", .close = ">")
+  pattern = glue::glue(
+    "^# <pkg_name> <version> [_\\*]20\\d{2}-\\d{2}-\\d{2}[_\\*]$",
+    .open = "<",
+    .close = ">"
+  )
   if (stringr::str_detect(news[1], pattern = pattern, negate = TRUE)) {
-    msg = glue::glue("Top line of NEWS.md not have correct format. It should be
-                       # {pkg_name} {version} _{Sys.Date()}_")
+    msg = glue::glue(
+      "Top line of NEWS.md not have correct format. It should be
+                       # {pkg_name} {version} _{Sys.Date()}_"
+    )
     msg_error(msg)
   } else {
     cli::cli_alert_success("Your NEWS.md has the correct format")
@@ -13,8 +18,10 @@ check_news_major = function(news, pkg_name, version) {
 check_news_minor = function(news, pkg_name, version) {
   pattern = glue::glue("^# {pkg_name} \\(development version\\)$")
   if (stringr::str_detect(news[1], pattern = pattern, negate = TRUE)) {
-    msg = glue::glue("Top line of NEWS.md not have correct format. It should be
-                       # {pkg_name} (development version)")
+    msg = glue::glue(
+      "Top line of NEWS.md not have correct format. It should be
+                       # {pkg_name} (development version)"
+    )
     msg_error(msg)
   } else {
     cli::cli_alert_success("Your NEWS.md has the correct format")
@@ -45,7 +52,7 @@ check_news = function(pattern = NULL, path = ".") {
   } else {
     check_news_minor(news, pkg_name, version)
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }
 
 
@@ -67,5 +74,5 @@ check_all_news = function(pattern = NULL) {
   } else {
     cli::cli_alert_success("Your NEWS.md has the correct format")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }

R/check_pkg.R

@@ -16,11 +16,18 @@ check_pkg = function(path = ".") {
   ## Install package dependencies
   cli::cli_h2("Installing package")
   remotes::install_deps(path, dependencies = TRUE, upgrade = "never")
-  remotes::install_local(path, upgrade = "never", build_vignettes = TRUE, force = TRUE)
+  remotes::install_local(
+    path,
+    upgrade = "never",
+    build_vignettes = TRUE,
+    force = TRUE
+  )
 
-  check_output = rcmdcheck::rcmdcheck(path = ".",
-                                      args = c("--timings"), # Add option for as--cran?
-                                      error_on = "error")
+  check_output = rcmdcheck::rcmdcheck(
+    path = ".",
+    args = c("--timings"), # Add option for as--cran?
+    error_on = "error"
+  )
   check_output = rcmdcheck::check_details(check_output)
 
   allowed_notes = get_env_variable("ALLOWED_NOTES", 0)
@@ -43,5 +50,5 @@ check_pkg = function(path = ".") {
   if (no_of_warnings > allowed_warnings || no_of_notes > allowed_notes) {
     msg_error("You have too many WARNINGS and/or NOTES")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }