NEWS

---

checklist 0.5.3

• Add publisher to .zenodo.json (#180).
• Add grant ID for EU-funded Zenodo communities (#182).
• Correctly handle ROR (#184)
• Fix Zenodo DOI badge in README.

checklist 0.5.2

• Only create the contributing guidelines or code of conduct file when the user answers "yes" on the related questions.

checklist 0.5.1

• bugfix in check_license() which failed when no correct license information is available in README.md (#166).
• The check_project GitHub Action now restores the R environment using renv when a renv.lock file is present. It also gains an APTGET argument to install system dependencies via apt-get.

checklist 0.5.0

Breaking changes

• The organisation class is superseded by the org_list and org_item classes.
• Updated the vignette("organisation", package = "checklist") to reflect the changes in the organisation class.
• organisation class and its related function like default_organisation(), read_organisation() and write_organisation() are deprecated.
• The new org_list enforces the use of the INBO ROR (#153).

New functions

• get_default_org_list() returns the default organisation list depending on the git remote origin.
• new_org_list() creates a new org_list object based on interactive questions.
• create_draft_pr() creates a draft pull request on GitHub.

Other changes

• create_package() and create_project() now fully work based on interactive questions.
• Updated the formatting of the code with air.
• The GitHub Actions now install missing packages on the fly (#152).
• Improved output on missing warning and notes (#155).
• check_folders() now handles nested folders (#156).
• check_project() now works on GitHub Actions with projects using renv (#158).
• check_lintr() turns missing dependencies into an error.
• check_source() is now defunct.
• Removed the defunct orcid2person().
• Reworked the vignette("philosophy", package = "checklist") and vignette("getting_started", package = "checklist")

checklist 0.4.2

• check_lintr() checks for missing dependencies.
• Checking projects on GitHub Actions try to install the missing dependencies.
• check_lintr() includes lintr::indentation_linter().
• Increase the time-out in check_cran().
• Docker image installs the latest version of TeXLive.
• Docker image installs missing packages on the fly.
• check_filename() ignores symbolic links.
• When the path is a git repository, check_filename() and check_folder() only check the files and directories under version control.
• check_folder() allows quarto specific _extensions and _files folders.
• citation_meta() now supports quarto documents.
• Improved support for quarto documents in check_spelling().
• add_badges() can create a version badge.
• create_draft_pr() returns the URL of the draft pull request.
• Fix bug in use_author() (#149).

checklist 0.4.1

• Add new function create_draft_pr().
• Escape quotes in the CITATION file.
• Install packages in Dockerfile using pak.
• check_description() doesn't require a funder when not set in the organisation.
• check_document() handles unexported functions in the documentation.
• check_lintr() requires the cyclocomp package.
• Improved extraction of citation information.
• Fix false positive from check_spelling() as requested in #147.
• Improve author2df().

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 of the Research Institute for Nature and Forest (INBO). See vignette("organisation", package = "checklist") for more information.
• The output of the check shows the git diff (#77).
• add_badges() helps to add badges to the README.
• Put double quotes around the title and abstract fields of CITATION.cff.
• check_documentation() handles assignment functions and re-exported functions correctly.
• check_lintr() ignores renv subdirectories (#118).
• Update to zen4R version 0.10 to reflect the Zenodo API changes (#125).
• update_citation() no longer introduces new lines (#124) and handles single quotes in titles (#115).
• You can add multiple affiliations per author (#123). Separate them by a semi-colon (;) in a DESCRIPTION or the yaml of a bookdown. Use multiple footnotes is a README.md.
• check_spelling() handles leading or trailing backwards slashes (#107).
• check_cran() ignores irrelevant CRAN notes.

checklist 0.3.5

• Fix release GitHub Action.
• Bugfix in update_citation() on a DESCRIPTION.
• check_spelling() handles Roxygen2 tags @aliases, @importMethodsFrom, @include, @keywords, @method, @name, @slot

checklist 0.3.4

• check_spelling() ignores numbers.
• Ask which GitHub organisation to use when create a new project. Default equals the organisation's default.
• GitHub Action for project allow to install package prior to checking the project. Use this in case check_lintr() returns an error about global variables in a function and you did require() the package.
• Fix release GitHub Action.

checklist 0.3.3

• New organisation() class to hold the requirements of the organisation. For the time being this is hard-coded to the Research Institute for Nature and Forest (INBO).
• Author affiliations must match one of the affiliations set in organisation(). The membership of an author is determined by their e-mail or their affiliation. This is checked when creating or using author information and when updating citation information.
• read_checklist() looks for checklist.yml in parent folders when it can't find it in the provided path.
• validate_orcid() checks the format and the checksum of the ORCID.
• Add vignette("folder", package = "checklist").

checklist 0.3.2

• citation_meta() gains support for bookdown reports.
• Add bookdown_zenodo() which first extracts the citation metadata from the yaml header. Then it cleans the output folder and renders the required output formats. Finally it uploads the rendered files to a draft deposit on Zenodo.
• setup_project() and create_project() provides support for renv.

checklist 0.3.1

• Fixes two bugs in case MIT license was chosen
• GitHub Actions now uses the latest version of checklist as default when checking packages or projects.

checklist 0.3.0

• Improved create_project() and setup_project() which interactively guides the user through the set-up.
• Add vignette("getting_started_project", package = "checklist").
• Improved GitHub Actions. They use the built-in GITHUB_TOKEN. The user only needs to set the CODECOV_TOKEN in case of a package.
• Fixes a note about "MIT" license.
• The Dockerimage uses the same dictionaries as the local installation.
• Add a German dictionary?
• Spell check roxygen2 tags in .R files.
• Don't spell check .Rd files generated by roxygen2.
• check_cran() ignores Days since last update note.
• check_documentation() yields a warning when it find documented but unexported function. Use the @noRD tag in case you still want to document the function without exporting it.
• Improved error messages for check_news().
• check_source() is now deprecated. Use check_project() instead.
• Parse DESCRIPTION (for a package) or README.md (for a project) to extract citation information into a citation_meta object. Then export this object into the different citation files.
• Standardise the DESCRIPTION and README.md to accommodate all citation information. DESCRIPTION gains checklist specific settings like Config/checklist/communities and Config/checklist/keywords.
• Store author information to reuse when running create_package() or create_project().
• Add check_folder().

checklist 0.2.6

• check_license() allows "MIT" license in addition to "GPLv3" for packages

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 [ISO 639-3 code] (https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Languages/List_of_ISO_639-3_language_codes_(2019)).
• create_package() gains a required language argument. This adds the required Language field to the DESCRIPTION.
• checklist objects gain an update_keywords method. This is currently only relevant for packages. Usage: check your package with x <- check_package(). Add keywords with x$update_keywords(c("keyword 1", "keyword 2"). The method adds the keyword "R package" automatically. Store the keywords with write_checklist(x). Run update_citation() to update the citation files with the keywords. Use x$get_keywords() to retrieve the current keywords.
• Improve the extraction of the DOI from the URL field.
• Allow .rda files in the inst folder of a package.
• Allow back ticks around package name in NEWS.md.
• Add prepare_ghpages().
• check_cran() ignores the insufficient package version when checking the main branch. This required when checking an R package when the current version equals the latest version on CRAN.
• Define explicit which lintr options to use.

checklist 0.2.3

• Add vignette("zenodo") on how to set up the integration with Zenodo and ORCID
• check_environment() makes sure that the required repository secrets are set. check_package() performs this check when it runs in a GitHub Action. A missing repository secret results in an error. It points to vignette("getting_started") which indicates how to solve it.

Bugfix

• Fix problem in write_zenodo_json() which produced a .zenodo.json which failed to parse on https://zenodo.org.
• write_zenodo_json() and write_citation_cff() return the checklist object and pass it to update_citation().

checklist 0.2.2

Bugfix

• Update URLS to lintr.

checklist 0.2.1

Bugfix

• Fixed git diff used by check_description() when checking for changes in version number.

checklist 0.2.0

• Migrate from 'git2r' to gert to communicate with Git and GitHub

Bugfix

• update_package() escapes double quotes in the abstract of inst/CITATION.
• Docker image uses the development version of lintr
• check_source() handles projects with renv on GitHub Actions.

checklist 0.1.14

• Improve error message when changes in CITATION need to be commit. (#64)
• create_package() can use maintainer information stored in the options. 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.

Bugfix

• create_package() replaces package name place holder with actual package name in _pkgdown.yml.

checklist 0.1.13

• A new function update_citation() creates or updates a default citation in inst/CITATION.
• When INBO is not listed as copyright holder, check_description() returns a warning rather than an error. This implies that you can motivate to ignore it via write_checklist(). (#33)
• Ignore all .Rd files when running check_filename(). (#59)
• check_filename() allows R/sysdata.rda. (#62)

checklist 0.1.12

User visible changes

• New new_branch() function to start a new branch from the most recent version of the main branch. This function will run clean_git() before creating the new branch.
• check_package() runs the pkgdown::build_site() by default in interactive sessions. The function gains a pkgdown argument to turn of this behaviour.

Bugfixes

• check_filename() handles git repositories without commits.
• check_filename() ignores Rd files. 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.

Package management

• Add Docker build tests.
• check_filename() ignores docker-compose files.

checklist 0.1.11

• Exclude renv and packrat folders from check_lintr().
• GitHub Actions bash script for packages checks out the main branch before setting tags.
• Install codemetar from GitHub because is it not available from CRAN.
• Install devtools from CRAN as the relevant version in available on CRAN.
• Add GitHub Action to automatically remove artefacts. This is required to keep the used storage to a minimum.
• Checks on different OS's only halt on errors. Because importing codemetar from GitHub results in a warning.
• Don't install dependencies automatically in the Dockerfile. This triggers an error when a dependency is not listed in the Dockerfile.
• pkgdown ensures that the reference page lists all exported functions.
• New pkgdown cascading style sheet.
• Bugfix in clean_git().

checklist 0.1.10

User visible changes

• Add clean_git() to bring a local git repo up-to-date.
  • Bring local branches up-to-date when there are behind the origin.
  • 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 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.
• Minor bugfix in entrypoint_package.sh.

checklist 0.1.9

User visible changes

• Many communities, both on GitHub and in the wider Git community, are considering renaming the default branch name of their repository from master. GitHub is gradually renaming the default branch of our own repositories from master to main. Therefore checklist now allows both a main or master branch as default. In case both are present, checklist uses main. Using only a master branch yields a note. Hence you must either which to a main branch or allow the note with write_checklist() (#44).

Bugfixes

• Convert fancy single quotes to neutral single quotes (#42).
• Fix check_description().

checklist 0.1.8

• Create a release when pushing a tag starting with v. We use a GitHub Action to create the release instead of an R function.
• New function: setup_source() to setup projects with only source files.
• Add auxiliary function create_hexsticker().
• Update check_filename() rules
  • Allow a data-raw folder
  • Allow more default GitHub file names
  • Ignore font files
  • csl files must follow the rules for graphics files
• create_package() adds
  • URL and BugReports to DESCRIPTION
  • GitHub Actions
  • basic setup for pkgdown.
• setup_package() updates .Rbuildignore and basic setup for pkgdown.
• Add more documentation on all functions.
• Add two vignettes:
  • vignette("getting_started")
  • vignette("philosophy")
• Use Ubuntu 18.04 instead of the end of life Ubuntu 16.04 when checking the package on the previous R release (#31).

checklist 0.1.7

• Pushing to master should automatically create a release, using set_tag().
• Add a Zenodo DOI badge to the README and DOI URL to DESCRIPTION.
• check_description() now checks authors (#7).
  • INBO is set as copyright holder and funder.
  • Every author has an ORCID.
• setup_package() adds the required files for a pkgdown website (#21).

checklist 0.1.6

• Drop the codemeta.json file. It requires constant updating as it contains a package file size.

checklist 0.1.5

• check_documentation() allows NEWS.md to have level 2 headings (##) and single line subitems ( *). It doesn't count URLs when determining the line of a line. 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 filename cran-comment.md and WORDLIST.
  • Allows man-roxygen as folder name.
  • Requires underscore (_) as separator for non-graphics files.
  • Requires dash (-) as separator for graphics files.
  • Basename separator issue are warnings instead of errors. So you can allow these warnings via write_checklist().
• Fix deploying pkgdown website and release.
• Package require a codemeta.json as written by codemetar::write_codemeta. Suggestions by codemetar to improve the package become checklist notes.
• set_tag() fails when in a detached HEAD state.
• set_tag() creates a release when a tag is created on GitHub.
• check_cran() ignores system time check when world clock API is not available.
• check_license() verifies the license information of a package. This check is included via check_description() in check_package().

checklist 0.1.4

• set_tag() skips if the tag already exists.
• create_package() sets a code of conduct and contributing guidelines.
• create_package() sets LICENSE.md.
• Run pkgdown::build_site() during the check_pkg GitHub action.
• Deploy the pkgdown website to a gp-pages branch when pushing to master during the check_pkg GitHub action.

checklist 0.1.3

• Add validate_email() to check for valid email addresses.
• Add orcid2person() which converts a valid ORCID into a person object.
• Add create_package() which prepare an RStudio project with an empty package.

checklist 0.1.2

• Correctly check the package version on the master branch and during rebasing.
• Updating the master branch will set a tag with the current version.

checklist 0.1.1

• Added a NEWS.md file to track changes to the package.
• Added a README.Rmd file with installation instructions.
• Rework checklist_template() into write_checklist().
• Add check_description().
• Add check_documentation().
• Add check_filename().
• Add check_source().
• check_lintr() also works on source code repositories.
• Activate GitHub action inbo/check_package.

checklist 0.1.0

• Initial version.
• Create checklist R6 class.
• Add check_cran().
• Add check_lintr().
• Add check_package().
• Add read_checklist().
• Add checklist_template().
• Add Dockerimage for GitHub actions.