workflowr/workflowr: workflowr 1.7.0

This minor release includes some new features, improved documentation, and bug fixes. Minor improvements New argument combine for wflow_build() and wflow_publish(). When Rmd files are specified with the argument files, they are built in addition to any Rmd files that are automatically built when setting arguments like make = TRUE and republish = TRUE. If you would instead like to only build Rmd files that are included in all the filters, you can set combine = "and" to take the intersection. For example, if you ran wflow_build("analysis/example*.Rmd", make = TRUE, combine = "and"), then this would only build those Rmd files matched by the file glob analysis/example*.Rmd and had been modified more recently than their corresponding HTML file. With the default, combine = "or", this would have built all the files that matched the file glob in addition to any files that had been modified more recently than their corresponding HTML file, even if they didn't match the file glob pattern (idea from @bfairkun in #221, implementation by @zaynaib in #227, #228) If wflow_publish() is called, but was not instructed which files to publish, it now throws an error. In other words, you must specify the files you wish to publish or use one of the convenience arguments like republish = TRUE or update = TRUE. It's previous behavior was to complete without having done anything, which was misleading (idea from @stephens999) It is now easier to enter commit messages with a separate title and body. If you pass a character vector to the argument message to any of the functions that perform a commit, e.g. wflow_publish(), the first element will be used as the title, and any subsequent elements will be separate paragraphs in the commit body. Using a separate title and body will improve the display of your commit messages on GitHub/GitLab and git log --oneline since these only show the title (suggestion from @LearnUseZone in #222, implementation by @zaynaib in #225) New argument only_published for wflow_toc(). If set to FALSE, then the table of contents will also include unpublished files (implemented by @giocomai in #234) Updated documentation Improved organization of reproducible research workshop vignette (thanks to @stephens999) Added more documentation to wflow_build() to explain when it does and doesn't load code defined in a .Rprofile file (idea from @pcarbo) Bug fixes Bug fix: Now workflowr will detect any problems with its dependencies when it is attached. All dependencies must be installed, loadable, and meet the minimum required version. Broken packages were causing cryptic, misleading errors (reported by in @markellekelly in #216 and @LearnUseZone in #217) Bug fix: wflow_quickstart() can now handle relative paths to the Rmd files when the working directory is changed (change_wd = TRUE, which is the default) Remove Rd warnings when installing package on Windows by explicitly specifying the topic page when cross-referencing an exported function from another package. Note that the links worked previously, so this change is just being proactive in case this warning starts getting strongly enforced. If the authors of the other package rearrange how they group functions into documentation topics, this will break the cross-references and require an update. See this thread for more details Bug fix: wflow_use_github() and wflow_use_gitlab() now use Font Awesome 5 syntax to insert icons into the navigation bar when a recent version of rmarkdown is installed (>= 2.6) (bug report from @christianholland, #231) Bug fix: wflow_open() no longer sends a warning if you are using bookdown::html_document2 as your primary output format in _site.yml with base_format: workflowr::wflow_html (bug report from @rgayler, #233) Miscellaneous Removed function wflow_update(). Its only purpose was to migrate projects created with [workflowrBeta][], which is now over 3 years old Bump minimum required version of R from 3.2.5 to 3.3.0. While workflowr itself should be able to continue to work fine with R 3.2.5, it was becoming too much of a burden to regularly test workflowr with R 3.2.5 as the RStudio engineers have started updating their packages to require a minimum of R 3.3.0 Require minimum versions of callr 3.7.0, knitr 1.29, rmarkdown 1.18 Switched to the workflowr repository itself to use the default branch "main" and changed the owner to the workflowr organization. This has no effect on workflowr projects (future or existing). It mainly affects contributors to workflowr development. However, please update any links you might have bookmarked (e.g. to documentation