jdblischak/workflowr: workflowr 1.5.0
Creators
- 1. University of Chicago
- 2. @storyscript
- 3. UC-Denver Anschutz Medical Campus
- 4. @weecology, Univ of Florida
- 5. Agios Pharmaceuticals
Description
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 functionwflow_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 tointeractive()
(i.e. it isTRUE
only if it is an interactive R session). This option is currently used bywflow_build()
,wflow_git_push()
, andwflow_publish()
.
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 reportIf 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:
workflowr:
suppress_report: TRUE
Many thanks to @kaneplusplus for implementing this feature! (#168)
Minor improvements and bug fixesRequire 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()
ifindex.Rmd
is missing the workflowr-specific site generatorwflow_site()
(idea from @pcarbo, #177)Fail early if missing required file
index.Rmd
Add argument
fail
towflow_git_pull()
with default value ofTRUE
. 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 setfail = 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 settinginclude_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 https://github.com/new (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 >=1.3.0Added httpuv as imported dependency so that
wflow_use_github()
is able to automatically create the GitHub repository via the httr packageSet (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.
Files
jdblischak/workflowr-v1.5.0.zip
Files
(838.8 kB)
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Additional details
Related works
- Is supplement to
- https://github.com/jdblischak/workflowr/tree/v1.5.0 (URL)