Merge pull request #90 from inbo/keyword

add spell checking support

.Rbuildignore

@@ -1,22 +1,22 @@
-^_pkgdown.yml$
 ^.*\.Rproj$
 ^.*\.zenodo.json$
 ^.dockerignore$
+^CITATION\.cff$
+^Dockerfile$
+^LICENSE.md$
+^README\.Rmd$
+^\.Rproj\.user$
 ^\.github$
 ^\.httr-oauth$
-^\.Rproj\.user$
 ^\.zenodo\.json$
+^_pkgdown.yml$
 ^checklist.yml$
-^CITATION\.cff$
 ^codecov\.yml$
 ^codemeta\.json$
 ^data-raw$
-^docker-compose.test.yml$
 ^docker$
-^Dockerfile$
+^docker-compose.test.yml$
 ^docs$
-^LICENSE.md$
 ^man-roxygen$
 ^pkgdown$
-^README\.Rmd$
 ^test_docker.sh$

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.2.4",
+  "version": "0.2.5",
   "description": "An opinionated set of rules for R packages and R source code projects.",
   "creators": [
     {
@@ -38,5 +38,8 @@
     }
   ],
   "language": "eng",
-  "keywords": "R package"
+  "keywords": [
+    "R package",
+    "quality control"
+  ]
 }

CITATION.cff

@@ -11,7 +11,7 @@ contact:
 - email: info@inbo.be
   name: Research Institute for Nature and Forest
 title: 'checklist: A Thorough and Strict Set of Checks for R Packages and Source Code'
-version: 0.2.4
+version: 0.2.5
 abstract: An opinionated set of rules for R packages and R source code projects.
 license: GPL-3.0
 type: software
@@ -20,4 +20,6 @@ repository-code: https://github.com/inbo/checklist
 identifiers:
 - type: url
   value: https://inbo.github.io/checklist/
-keywords: R package
+keywords:
+- R package
+- quality control

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.2.4
+Version: 0.2.5
 Authors@R: c(
     person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216")),
@@ -20,17 +20,20 @@ BugReports: https://github.com/inbo/checklist/issues
 Depends:
     R (>= 3.5.0)
 Imports:
-    R6,
     assertthat,
     codemetar,
     desc,
     devtools (> 2.4.0),
+    fs,
     gert,
     httr,
+    hunspell,
     jsonlite,
     lintr (>= 2.0.1.9000),
     pkgdown,
+    R6,
     rcmdcheck,
+    renv,
     rmarkdown,
     rorcid,
     sessioninfo,
@@ -39,17 +42,17 @@ Imports:
     yaml
 Suggests:
     covr,
+    curl,
     knitr,
     mockery,
     roxygen2,
+    rstudioapi,
     showtext,
     sysfonts,
     testthat
 VignetteBuilder: 
     knitr
-Remotes: 
-    r-lib/lintr
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1

Dockerfile

@@ -51,7 +51,7 @@ RUN apt-get update \
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("hunspell")'
 
 ## install lintr
-RUN Rscript --no-save --no-restore -e 'remotes::install_github("r-lib/lintr")'
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("lintr")'
 
 ## install microbenchmark
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("microbenchmark")'
@@ -90,7 +90,14 @@ RUN Rscript --no-save --no-restore -e 'remotes::install_cran("rmarkdown")'
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("rorcid")'
 
 ## install spelling
-RUN Rscript --no-save --no-restore -e 'remotes::install_cran("spelling")'
+RUN apt-get update \
+  && apt-get install  -y --no-install-recommends \
+    hunspell-de-de \
+    hunspell-en-gb \
+    hunspell-fr \
+    hunspell-nl \
+  && apt-get clean \
+  && Rscript --no-save --no-restore -e 'remotes::install_cran("hunspell")'
 
 ## install spelling
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("withr")'
@@ -101,4 +108,5 @@ RUN Rscript --no-save --no-restore -e 'remotes::install_local("checklist", upgra
 
 COPY docker/entrypoint_package.sh /entrypoint_package.sh
 COPY docker/entrypoint_source.sh /entrypoint_source.sh
+COPY docker/entrypoint_project.sh /entrypoint_project.sh
 ENTRYPOINT ["/entrypoint_package.sh"]

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,checklist_language)
+S3method(print,checklist_spelling)
+export(c_sort)
 export(check_codemeta)
 export(check_cran)
 export(check_description)
@@ -9,11 +12,15 @@ export(check_filename)
 export(check_license)
 export(check_lintr)
 export(check_package)
+export(check_project)
 export(check_source)
+export(check_spelling)
 export(checklist)
 export(clean_git)
 export(create_hexsticker)
 export(create_package)
+export(create_project)
+export(custom_dictionary)
 export(is_repository)
 export(is_workdir_clean)
 export(new_branch)
@@ -22,7 +29,9 @@ export(prepare_ghpages)
 export(read_checklist)
 export(set_tag)
 export(setup_package)
+export(setup_project)
 export(setup_source)
+export(spelling)
 export(tidy_desc)
 export(update_citation)
 export(validate_email)
@@ -44,6 +53,24 @@ importFrom(desc,desc)
 importFrom(desc,description)
 importFrom(devtools,build_readme)
 importFrom(devtools,document)
+importFrom(fs,dir_create)
+importFrom(fs,dir_exists)
+importFrom(fs,dir_ls)
+importFrom(fs,file_copy)
+importFrom(fs,file_exists)
+importFrom(fs,file_move)
+importFrom(fs,is_dir)
+importFrom(fs,is_file)
+importFrom(fs,path)
+importFrom(fs,path_common)
+importFrom(fs,path_dir)
+importFrom(fs,path_ext_remove)
+importFrom(fs,path_filter)
+importFrom(fs,path_has_parent)
+importFrom(fs,path_norm)
+importFrom(fs,path_real)
+importFrom(fs,path_rel)
+importFrom(fs,path_split)
 importFrom(gert,git_add)
 importFrom(gert,git_ahead_behind)
 importFrom(gert,git_branch)
@@ -76,15 +103,24 @@ importFrom(grDevices,svg)
 importFrom(graphics,plot.new)
 importFrom(graphics,text)
 importFrom(httr,HEAD)
+importFrom(hunspell,dictionary)
+importFrom(hunspell,hunspell)
+importFrom(hunspell,list_dictionaries)
 importFrom(jsonlite,toJSON)
 importFrom(lintr,lint_dir)
 importFrom(lintr,lint_package)
 importFrom(pkgdown,build_site)
 importFrom(rcmdcheck,rcmdcheck)
+importFrom(renv,dependencies)
 importFrom(rmarkdown,pandoc_exec)
 importFrom(rorcid,as.orcid)
 importFrom(sessioninfo,session_info)
+importFrom(stats,aggregate)
 importFrom(stats,na.omit)
+importFrom(stats,setNames)
+importFrom(tools,RdTextFilter)
+importFrom(tools,loadPkgRdMacros)
+importFrom(tools,loadRdMacros)
 importFrom(tools,toTitleCase)
 importFrom(utils,browseURL)
 importFrom(utils,file_test)
@@ -93,6 +129,7 @@ importFrom(utils,installed.packages)
 importFrom(utils,menu)
 importFrom(utils,person)
 importFrom(utils,tail)
+importFrom(utils,unzip)
 importFrom(withr,with_path)
 importFrom(yaml,read_yaml)
 importFrom(yaml,write_yaml)

NEWS.md

@@ -1,3 +1,13 @@
+# checklist 0.2.5
+
+* Add spell checking functionality.
+  See `vignette("spelling", package = "checklist")` for more details.
+* The `checklist` class stores the required checks.
+* Add `setup_project()` to set-up `checklist` on an existing project.
+  This function allows the user to choose which checks to be required.
+* Add `check_project()` to run the required checks of a project.
+* Fix bug in `.zenodo.json` when only one keyword is present.
+
 # checklist 0.2.4
 
 * `check_description()` enforces a `Language` field with a valid
@@ -68,7 +78,7 @@
   See `usethis::use_description()` on how to set the option.
 * Add R universe badges to README.
 * Add `write_zenodo_json()` and `write_citation_cff()`.
-* Improve the checklist Github Actions.
+* Improve the checklist GitHub Actions.
 
 ## Bugfix
 
@@ -100,7 +110,7 @@
 
 * `check_filename()` handles git repositories without commits.
 * `check_filename()` ignores Rd files.
-  They have use a different naming convention when generated by Roxygen2. 
+  They have use a different naming convention when generated by roxygen2. 
 * `clean_git()` yields cleaner warnings.
 * `create_hexsticker()` will create the target directory when it doesn't exist.
 
@@ -135,14 +145,15 @@
     * Remove remote branches when removed from the origin.
     * Remove local branches when fully merged into the main branch.
     * Warn for diverging branches.
-* `create_hexsticker()` yields an svg file instead of png.
-  The user can optionally specify an svg icon file to add to the hexsticker.
+* `create_hexsticker()` yields an `svg` file instead of `png`.
+  The user can optionally specify an `svg` icon file to add to the hexagonal
+  sticker.
 * Keep failed build artefacts only 14 days (https://github.com/inbo/tutorials/issues/251).
 
 ## Bugfixes
 
 * Avoid false positive linters when `.Rproj` file is put under version control.
-* `check_files()` considers files with svg extensions as graphical files.
+* `check_files()` considers files with `svg` extensions as graphical files.
 * Minor bugfix in `entrypoint_package.sh`.
 
 # checklist 0.1.9
@@ -175,7 +186,7 @@
     * Allow a `data-raw` folder
     * Allow more default GitHub file names
     * Ignore font files
-    * csl files must follow the rules for graphics files
+    * `csl` files must follow the rules for graphics files
 * `create_package()` adds
     * URL and BugReports to `DESCRIPTION`
     * GitHub Actions
@@ -211,7 +222,7 @@
   This allows lines to be longer than 80 characters due to long URLs.
 * `check_filename()` is more liberal.
     * Allows files ending on `-package.Rd`.
-    * Allows json or yml files starting with a dot and followed by letters.
+    * Allows `json` or `yml` files starting with a dot and followed by letters.
     * Allows filename `cran-comment.md` and `WORDLIST`.
     * Allows `man-roxygen` as folder name.
     * Requires underscore (`_`) as separator for non-graphics files.

R/c_sort.R

@@ -0,0 +1,21 @@
+#' Sort using the C locale
+#'
+#' Setting the locale before sorting ensures a stable sorting order
+#' @inheritParams base::sort
+#' @export
+#' @family utils
+c_sort <- function(x, ...) {
+  old_ctype <- Sys.getlocale(category = "LC_CTYPE")
+  old_collate <- Sys.getlocale(category = "LC_COLLATE")
+  old_time <- Sys.getlocale(category = "LC_TIME")
+  Sys.setlocale(category = "LC_CTYPE", locale = "C")
+  Sys.setlocale(category = "LC_COLLATE", locale = "C")
+  Sys.setlocale(category = "LC_TIME", locale = "C")
+  on.exit(Sys.setlocale(category = "LC_CTYPE", locale = old_ctype), add = TRUE)
+  on.exit(
+    Sys.setlocale(category = "LC_COLLATE", locale = old_collate),
+    add = TRUE
+  )
+  on.exit(Sys.setlocale(category = "LC_TIME", locale = old_time), add = TRUE)
+  sort(x, ...)
+}

R/check_codemeta.R

@@ -2,7 +2,7 @@
 #'
 #' Use the checks from [codemetar::give_opinions()].
 #' @inheritParams read_checklist
-#' @return A `Checklist` object.
+#' @return A `checklist` object.
 #' @importFrom assertthat assert_that
 #' @importFrom codemetar give_opinions
 #' @importFrom gert git_status
@@ -26,9 +26,11 @@ check_codemeta <- function(x = ".") {
     "Code metadata needs to be updated. Run `codemetar::write_codemeta()`."[
       !unchanged_repo(repo, status_before)
     ],
-    "codemeta"
+    item = "codemeta", keep = FALSE
+  )
+  x$add_notes(
+    sprintf("in %s fix %s", opinions$where, opinions$fixme), "codemeta"
   )
-  x$add_notes(sprintf("in %s fix %s", opinions$where, opinions$fixme))
 
   return(x)
 }

R/check_cran.R

@@ -6,7 +6,7 @@
 #' Notice that `check_package()` runs several additional tests.
 #' @inheritParams read_checklist
 #' @inheritParams rcmdcheck::rcmdcheck
-#' @return A `Checklist` object.
+#' @return A `checklist` object.
 #' @importFrom assertthat assert_that
 #' @importFrom gert git_ahead_behind git_branch_exists git_info
 #' @importFrom httr HEAD