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jdblischak/workflowr: workflowr 1.5.0

John Blischak; Peter Carbonetto; Jiaxiang Li; Zaynaib (Ola) Giwa; Wouter van Amsterdam; E. David Aja; Pierre Formont; Michael Kane; Tim Trice; Steve Peak; Luke Zappia; Josh Johnson; Ethan White; Ania Tassinari

This minor release of workflowr includes a new function, the introduction of options to control package-wide function behavior, the ability to suppress the workflowr report from the HTML file, a new vignette for teaching workflowr, and lots of error handling improvements.

New function wflow_quickstart()

The new function wflow_quickstart() provides a simple interface to effortlessly create a workflowr project from an existing data analysis. Pass it your existing R Markdown file(s), and it will start a new workflowr project, publish the analysis files, and configure GitHub (or GitLab).

wflow_quickstart(files = "existing-analysis.Rmd", username = "your-github-username")
Package options

This is the first release to include options for controlling the behavior of all workflowr functions. This makes it more convenient for you to create a consistent workflowr experience. You can set the options in your project's .Rprofile (using the function options()) instead of having to always remember to change a default argument every time you call a function.

Currently there are two workflowr package options. See ?workflowr for more details.

  • workflowr.git: Set the path to the system Git executable, which is occasionally used to increase the speed of Git operations performed by workflowr functions.

  • workflowr.view: Should workflowr functions open webpages for viewing in the browser? The default is set to interactive() (i.e. it is TRUE only if it is an interactive R session). This option is currently used by wflow_build(), wflow_git_push(), and wflow_publish().

Workshop tutorial for teaching workflowr

The new vignette "Reproducible research with workflowr" is designed to be taught as a tutorial in a workshop setting. It includes setup instructions, an example analysis to highlight the benefits of workflowr, and troubleshooting advice.

Suppress the HTML workflowr report

If you'd like to suppress the workflowr report at the top of an HTML page, you can set the option suppress_report to TRUE. To suppress the report in every HTML file, set the option in _workflowr.yml:

suppress_report: TRUE

To suppress the report in a specific HTML file, add the following to the YAML header of the corresponding Rmd file:

  suppress_report: TRUE

Many thanks to @kaneplusplus for implementing this feature! (#168)

Minor improvements and bug fixes
  • Require git2r >= 0.26.0 to support internal changes that increase speed and robustness of workflowr Git functionality

  • wflow_start() adds a .gitattributes file that classifies R Markdown files as R code for the official GitHub language statistics calculated via linguist. The default setting is to ignore R Markdown files.

  • Address callr 3.3.0 bug that writes objects to the global environment, causing the workflowr check of the global environment to fail. The failed check now explains that the problem can be fixed by updating the callr package.
  • Warn user from wflow_build() if index.Rmd is missing the workflowr-specific site generator wflow_site() (idea from @pcarbo, #177)

  • Fail early if missing required file index.Rmd

  • Add argument fail to wflow_git_pull() with default value of TRUE. Now if a pull generates a merge conflict, wflow_git_pull() will abort the pull. Thus no changes will be made to the local files. Users can set fail = FALSE to allow Git to add the merge conflicts to the local files.

  • Speed improvements for wflow_publish()

  • Improved error handling when files contain merge conflicts. Before workflowr only detected merge conflicts in Rmd files. Now it detects them for any file (since Git requires any merge conflicts to be resolved before it makes any new commits).

  • Warn user if knit_root_dir (the directory where the code in the Rmd files is executed) defined in _workflowr.yml is an absolute path. An absolute path would only work on the current computer, limiting reproducibility.

  • Include Git status in output of wflow_status(). Note that it purposefully excludes any files in the website directory since these generated files should only be committed by workflowr. You can omit the Git status by setting include_git_status = FALSE (idea from @pcarbo)

  • Make it clearer that you have two options for creating the remote repository on Github: 1) let wflow_use_github() do it automatically, or 2) create it yourself manually at (idea from @pcarbo)

  • New FAQ "How can I save a figure in a vector graphics format (e.g. PDF)?"

  • Added citation to F1000Research paper. Run citation("workflowr") to obtain the new citation information.

  • Fixed wflow_start() infinite recursion bug by requiring stringr >=1.3.0

  • Added httpuv as imported dependency so that wflow_use_github() is able to automatically create the GitHub repository via the httr package

  • Set (or increased) minimum required versions for fs, git2r, httpuv, rstudioapi, stringr, whisker, clipr, shiny, testthat, and withr

  • Document possible error of a greyed out GitHub authentication button when trying to give permission for workflowr to create a repository for your account

  • Fixed bug in date displayed in table of past versions in the workflowr report. Depending on the time of day the commit was made, the displayed day may have been off by one.

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