jdblischak/workflowr: workflowr 1.6.0

New features

• New function wflow_run(). It executes the code chunks of an R Markdown file in the current R session without affecting any of the website files. This is meant to be used while interactively developing an analysis. It does not change the working directory or isolate the computation from the current R session. This is analogous to the RStudio option "Run all" to run all the code chunks (idea from @pcarbo)

• New autosave feature. The workflowr functions wflow_build(), wflow_publish(), and wflow_status() will autosave any unsaved files open in the RStudio editor pane. This is similar to the behavior of the Knit HTML button. This feature can be disabled by setting the package option workflowr.autosave to FALSE (idea from @xiangzhu in #179)

• New vignette on using large data files in a workflowr project (motivated by @xiangzhu, #183)

• If there are merge conflicts after running wflow_git_pull(), and the merge was allowed to proceed (fail = FALSE), then the conflicted files are listed and optionally opened in RStudio at the first line of the conflict that needs to be resolved

• wflow_git_config() has a new argument overwrite. Previously wflow_git_config() would by default overwrite any previous settings. Now this will throw an error. To overwrite a previous setting, set overwrite = TRUE (idea from @petebaker)

• Warn user if only HTML file has been committed (and avoid throwing an error). Previously this threw an error because workflowr expects the R Markdown file to be committed to the Git repo if its corresponding HTML file is (bug report from @kevinlkx)

• Warn user if a dependency does not meet the minimum required version. There are multiple ways this could happen. First, it is possible to install an old version after having installed workflowr. Second, when running install.packages(), if the minimum required version is available in any of the package libraries, it is not installed. However, if the version of the package in the first directory listed in .libPaths() does not meet the minimum required version, it is still the one that is loaded when workflowr is loaded (idea from @stephens999)

• Fix off-by-one date bug by specifying the local timezone (see git2r Issue 407)

• Fix bug when path to project includes a space. The bug was introduced in version 1.5.0 with the feature to use the system Git executable to run git ls-files. To fix the issue in version 1.5.0, set options(workflowr.sysgit = "") in the file .Rprofile (bug report from @wolfemd, #180)

• Fix bug caused by an unset timezone. If the machine has no timezone set, workflowr will default to Etc/UTC

• Handle missing title/pagetitle warning from pandoc 2+ and rmarkdown 1.18+ (see rmarkdown Issue 1355)

• Improve speed of wflow_publish()/wflow_status() by using the system Git executable (if available) to obtain the last commit time of the analysis files (this is used to determine which published Rmd files are outdated and need to be republished)

• Report exact command to run git push or git pull in the terminal if either wflow_git_push() or wflow_git_pull() fail (reported by @jennysjaarda, #182)

• Update FAQ to include how to create a PDF using the RStudio Knit button (reported by @han16)

• Update citation to workflowr publication

• Properly quote the Git executable with shQuote() whenever Git is called from R