version 0.3.7

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.3.6",
+  "version": "0.4.0",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>An opinionated set of rules for R packages and R source code projects.<\/p>",

CITATION.cff

@@ -25,4 +25,4 @@ identifiers:
   value: 10.5281/zenodo.4028303
 - type: url
   value: https://inbo.github.io/checklist/
-version: 0.3.6
+version: 0.4.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.3.6
+Version: 0.4.0
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -59,5 +59,5 @@ Config/checklist/keywords: quality control; documentation; publication
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 SystemRequirements: Pandoc (>= 1.17.2)

Dockerfile

@@ -13,8 +13,8 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
       maintainer="Thierry Onkelinx <[email protected]>"
 
 ## for apt to be noninteractive
-ENV DEBIAN_FRONTEND noninteractive
-ENV DEBCONF_NONINTERACTIVE_SEEN true
+ENV DEBIAN_FRONTEND=noninteractive
+ENV DEBCONF_NONINTERACTIVE_SEEN=true
 
 ## Install nano
 RUN apt-get update \

LICENSE.md

@@ -1,4 +1,4 @@
-### GNU GENERAL PUBLIC LICENSE
+# GNU GENERAL PUBLIC LICENSE
 
 Version 3, 29 June 2007
 

NAMESPACE

@@ -37,6 +37,7 @@ export(organisation)
 export(prepare_ghpages)
 export(read_checklist)
 export(read_organisation)
+export(set_license)
 export(set_tag)
 export(setup_package)
 export(setup_project)

NEWS.md

@@ -1,3 +1,13 @@
+# checklist 0.4.0
+
+* Updated `README.md`.
+* Improved support for `organisation`.
+* Add `set_license()`.
+* `check_filename()` allows a `CODEOWNERS` file.
+* The checklist summary displays the unstaged git changes.
+* The GitHub Action on packages installs the `roxygen2` version listed in the
+  `DESCRIPTION` of the package it checks.
+
 # checklist 0.3.6
 
 * Add an `organisation` class to store organisation rules different from those

R/check_description.R

@@ -273,12 +273,12 @@
     official <- official[-3]
     current <- current[-3]
   }
-  problems <- c(
-      problems,
-      "LICENSE.md doesn't match the version in the checklist package"[
-        (length(current) != length(official)) || any(current != official)
-      ]
+  if ((length(current) != length(official)) || any(current != official)) {
+    problems <- c(
+      problems, "LICENSE.md doesn't match the version in the checklist package"
     )
+    set_license(x)
+  }
   x$add_error(
     errors = problems,
     item = "license", keep = FALSE
@@ -291,19 +291,46 @@
 check_authors <- function(this_desc, org) {
   assert_that(inherits(org, "organisation"))
   authors <- this_desc$get_authors()
-  stopifnot(
-    "TO DO: handle funder not equal to rightsholder" =
-      (is.na(org$get_rightsholder) && is.na(org$get_funder)) ||
-        (org$get_rightsholder == org$get_funder)
-  )
-  rightsholder <- person(
-    given = org$get_rightsholder, role = c("cph", "fnd"), email = org$get_email
+  email <- c(NULL, org$get_email[!is.na(org$get_email)])
+  if (!is.na(org$get_rightsholder)) {
+    if (!is.na(org$get_funder)) {
+      if (org$get_rightsholder == org$get_funder) {
+        rightsholder <- person(
+          given = org$get_rightsholder, role = c("cph", "fnd"), email = email
+        )
+        funder <- NULL
+      } else {
+        rightsholder <- person(
+          given = org$get_rightsholder, role = "cph", email = email
+        )
+        funder <- person(given = org$get_funder, role = "fnd")
+      }
+    } else {
+      rightsholder <- person(
+        given = org$get_rightsholder, role = "cph", email = email
+      )
+      funder <- NULL
+    }
+  } else if (!is.na(org$get_funder)) {
+    rightsholder <- NULL
+    funder <- person(given = org$get_funder, role = "fnd")
+  }
+
+  problems <- c(
+    sprintf(
+      "`%s` must be listed as copyright holder and use `%s` as email.",
+      org$get_rightsholder, org$get_email
+    )[
+      !is.null(rightsholder) && !is.na(org$get_rightsholder) &&
+        !rightsholder %in% authors
+    ],
+    sprintf(
+      "`%s` must be listed as funder without email.",
+      org$get_funder
+    )[!is.null(funder) && !is.na(org$get_funder) && !funder %in% authors]
   )
-  problems <- sprintf(
-    "`%s` must be listed as copyright holder and funder and use `%s` as email.",
-    org$get_rightsholder, org$get_email
-  )[!is.na(org$get_rightsholder) && !rightsholder %in% authors]
   authors <- authors[!authors %in% rightsholder]
+  authors <- authors[!authors %in% funder]
   vapply(
     authors, FUN.VALUE = vector(mode = "list", length = 1L),
     FUN = function(author) {

R/check_filename.R

@@ -98,7 +98,7 @@ check_filename <- function(x = ".") {
     paste(
       c(
         "\\.[a-zA-Z]+ignore", "\\.Rprofile", "\\.[a-zA-Z]+\\.(json|yml)",
-        "CITATION", "DESCRIPTION", "NAMESPACE", "CITATION\\.cff",
+        "CITATION", "CODEOWNERS", "DESCRIPTION", "NAMESPACE", "CITATION\\.cff",
         "README\\.R?md", "NEWS\\.md",
         "CODE_OF_CONDUCT\\.md", "CONTRIBUTING\\.md", "LICENSE(\\.md)?",
         "SUPPORT\\.md", "SECURITY\\.md", "FUNDING\\.yml",

R/check_spelling.R

@@ -243,7 +243,7 @@ rstudio_source_markers <- function(issues) { # nocov start
     "`%s` not found in the dictionary or wordlist for %s.", issues$message,
     issues$language
   )
-  issues <- issues[order(issues$file, issues$line, issues$column), ]
+  issues <- unique(issues[order(issues$file, issues$line, issues$column), ])
   issues$file <- as.character(issues$file)
   # request source markers
   rstudioapi::callFun(

R/citation_description.R

@@ -173,6 +173,7 @@ description_communities <- function(communities, org) {
     )
   }
   list(
-    meta = list(community = communities), warnings = character(0)
+    meta = list(community = split_community(communities)),
+    warnings = character(0)
   )
 }

R/citation_meta_class.R

@@ -173,13 +173,20 @@ validate_citation <- function(meta) {
   rightsholder_id <- roles$contributor[roles$role == "copyright holder"]
   funder_id <- roles$contributor[roles$role == "funder"]
   notes <- c(
+    "no rightsholder listed"[
+      !is.na(org$get_rightsholder) && length(rightsholder_id) == 0
+    ],
+    "no funder listed"[!is.na(org$get_funder) && length(funder_id) == 0],
     sprintf("rightsholder differs from `%s`", org$get_rightsholder)[
-      !is.na(org$get_rightsholder) &&
-        authors$given[authors$id == rightsholder_id] != org$get_rightsholder
+      !is.na(org$get_rightsholder) && length(rightsholder_id) >= 1 &&
+        !any(
+          authors$given[authors$id %in% rightsholder_id] %in%
+            org$get_rightsholder
+        )
     ],
     sprintf("funder differs from `%s`", org$get_funder)[
-      !is.na(org$get_funder) &&
-        authors$given[authors$id == funder_id] != org$get_funder
+      !is.na(org$get_funder) && length(funder_id) >= 1 &&
+        !any(org$get_funder %in% authors$given[authors$id == funder_id])
     ]
   )
   errors <- c(

R/create_package.R

@@ -185,23 +185,7 @@ create_package <- function(
   git_add("README.Rmd", repo = repo)
 
   # add LICENSE.md
-  license_file <- path(path, "LICENSE.md")
-  switch(
-    license, "GPL-3" = path("generic_template", "gplv3.md"),
-    "MIT" = path("generic_template", "mit.md")
-  ) |>
-    system.file(package = "checklist") |>
-    file_copy(license_file)
-  if (license == "MIT") {
-    paste0("YEAR: ", format(Sys.Date(), "%Y")) |>
-      c(sprintf("COPYRIGHT HOLDER: %s", org$get_rightsholder)) |>
-      writeLines(path(path, "LICENSE"))
-    git_add("LICENSE", repo = repo)
-    mit <- readLines(license_file)
-    mit[3] <- gsub("<YEAR>", format(Sys.Date(), "%Y"), mit[3])
-    mit[3] <- gsub("<COPYRIGHT HOLDER>", org$get_rightsholder, mit[3])
-    writeLines(mit, license_file)
-  }
+  set_license(x)
   git_add("LICENSE.md", repo = repo)
 
   # Add code of conduct

R/default_organisation.R

@@ -13,7 +13,9 @@
 #' @family both
 default_organisation <- function(org = organisation$new()) {
   assert_that(inherits(org, "organisation"))
-  R_user_dir("checklist", which = "config") |>
+  target <- R_user_dir("checklist", which = "config")
+  dir_create(target)
+  target |>
     path("organisation.yml") |>
     write_yaml(x = org$template)
   return(invisible(NULL))

R/organisation_class.R

@@ -25,10 +25,11 @@ organisation <- R6Class(
     #' - `rightsholder`: the rightsholder.
     #'   Defaults to `"Research Institute for Nature and Forest (INBO)"`.
     #'   Set to `NA_character_` in case you don't want to set a rightsholder.
-    #' - `organisation`: a named list with one or more organisation defaults.
+    #' - `organisation`: a named list with one or more organisation default
+    #'   rules.
     #'   The names of the element must match the e-mail domain name of the
     #'   organisation.
-    #'   Every element should be a named list containing ´affiliation` and
+    #'   Every element should be a named list containing `affiliation` and
     #'   `orcid`.
     #'   `affiliation` is a character vector with the approved organisation
     #'   names in one or more languages.

R/read_checklist.R

@@ -32,7 +32,12 @@ read_checklist <- function(x = ".") {
   }
   assert_that(
     is_file(checklist_file),
-    msg = sprintf("no checklist.yml found `%s` or its parents", x)
+    msg = paste(
+      "No checklist.yml found at `%1$s` or its parents.",
+      "\nRun `checklist::setup_package(\"%1$s\")` or",
+      "`checklist::setup_project(\"%1$s\")`."
+    ) |>
+      sprintf(path_real(x))
   )
 
   # read existing check list file

R/set_license.R

@@ -0,0 +1,51 @@
+#' Set the proper license
+#' @inheritParams read_checklist
+#' @family setup
+#' @export
+#' @importFrom assertthat assert_that
+#' @importFrom desc description
+#' @importFrom fs file_copy file_exists path
+set_license <- function(x = ".") {
+  x <- read_checklist(x = x)
+  license_file <- path(x$get_path, "LICENSE.md")
+  if (x$package) {
+    assert_that(
+      file_exists(path(x$get_path, "DESCRIPTION")),
+      msg = sprintf("No `DESCRIPTION` file found at %s", x$get_path)
+    )
+    this_desc <- description$new(file = path(x$get_path, "DESCRIPTION"))
+    assert_that(
+      this_desc$has_fields("License"),
+      msg = "`DESCRIPTION` has no `License`field."
+    )
+    switch(
+      this_desc$get_field("License"),
+      "GPL-3" = path("generic_template", "gplv3.md"),
+      "MIT" = path("generic_template", "mit.md"),
+      "MIT + file LICENSE" = path("generic_template", "mit.md"),
+      stop(
+        sprintf("`%s` license is not available", this_desc$get_field("License"))
+      )
+    ) |>
+      system.file(package = "checklist") |>
+      file_copy(license_file, overwrite = TRUE)
+    if (!grepl("^MIT", this_desc$get_field("License"))) {
+      return(invisible(NULL))
+    }
+    this_desc$get_author(role = "cph") |>
+      format(include = c("given", "family")) |>
+      paste(collapse = ", ") -> cph
+    paste0("YEAR: ", format(Sys.Date(), "%Y")) |>
+      c(sprintf("COPYRIGHT HOLDER: %s", cph)) |>
+      writeLines(path(x$get_path, "LICENSE"))
+    mit <- readLines(license_file)
+    mit[3] <- gsub("<YEAR>", format(Sys.Date(), "%Y"), mit[3])
+    mit[3] <- gsub("<COPYRIGHT HOLDER>", cph, mit[3])
+    writeLines(mit, license_file)
+    return(invisible(NULL))
+  }
+  path("generic_template", "cc_by_4_0.md") |>
+    system.file(package = "checklist") |>
+    file_copy(license_file, overwrite = TRUE)
+  return(invisible(NULL))
+}

R/setup_package.R

@@ -35,7 +35,16 @@
 
   # add checklist.yml
   if (!file_exists(path(path, "checklist.yml"))) {
-    x <- checklist$new(x = path, language = "en-GB", package = TRUE)
+    if (descript$has_fields("Language")) {
+      x <- checklist$new(
+        x = path, language = descript$get_field("Language"), package = TRUE
+      )
+    } else {
+      x <- checklist$new(x = path, language = "en-GB", package = TRUE)
+      descript$set("Language", "en-GB")
+      path(x$get_path, "DESCRIPTION") |>
+        descript$write()
+    }
     x$set_required()
     x$set_ignore(c(".github", "LICENSE.md"))
     write_checklist(x)

R/setup_project.R

@@ -54,10 +54,7 @@ setup_project <- function(path = ".") {
   x$set_default(c("en-GB", "nl-BE", "fr-FR")[answer])
 
   if ("license" %in% checks && !file_exists(path(path, "LICENSE.md"))) {
-    insert_file(
-      repo = repo, filename = "cc_by_4_0.md", template = "generic_template",
-      target = path, new_name = "LICENSE.md"
-    )
+    set_license(x)
   }
 
   x$set_required(checks = checks)

R/utils.R

@@ -331,17 +331,11 @@ checklist_diff <- function(root) {
   if (inherits(try(git_info(repo = root), silent = TRUE), "try-error")) {
     return(invisible(NULL))
   }
-  branch_info <- git_branch_list(repo = root)
-  branch_info$ref[
-    grep("/main$", branch_info$ref) |>
-      c(grep("/master$", branch_info$ref)) |>
-      head(1)
-  ] |>
-    git_diff(repo = root) -> changes
+  changes <- git_diff(repo = root)
   if (length(changes) == 0) {
     return(invisible(NULL))
   }
-  cli_h1("git diff")
+  cli_h1("unstaged changes")
   changes$patch |>
     gsub(pattern = "^.*?index.*?\n.*?\n", replacement = "") |>
     strsplit(split = "\n") |>