Organize your project into a research website
This patch release includes improved documentation, bug fixes, and a reduction in the number of Suggested dependencies.
Update single-page FAQ to explain how to remove navbar
Update badge links (implemented by @wyq977 in #276)
Explicitly label internal functions with roxygen2
Build online docs via GitHub Actions and push to gh-pages
Improve guidance on rendering a standalone HTML file in FAQ vignette (idea from @fkgruber in #283)
Add the appropriate PKGNAME-package \alias to the package overview help file as per "Documenting packages" in Writing R Extensions
Modernize CITATION. Replace citEntry() with bibentry(), replace
personList() with c(), format as R code, and simplify.
Fix missing figure version table on Windows (implemented by @warmdev in #275)
Use conditionMessage() to extract error message from callr subprocess
r-lib/callr#228
Remove warning from sprintf() in print.wflow_start() when git = FALSE
This minor release includes some new features, improved documentation, and bug fixes.
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)
wflow_build() to explain when it does and
doesn't load code defined in a .Rprofile file (idea from @pcarbo)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)
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)
This patch release of workflowr includes minor improvements, updated documentation, and bug fixes. Users are encouraged to upgrade workflowr so that it is compatible with the next release of fs (>1.4.1).
wflow_use_github() to the GitHub API more resilient to transient network issues by automatically retrying HTTP calls more than once (@jameslamb, #199, #201)wflow_start() (@trannhatanh89, #193, #200)overwrite = TRUE to wflow_start() but existing = FALSE, since it isn't possible to overwrite non-existent files (@skpurdue, #194, #202, idea from @pcarbo)public/, not docs/ (idea from @ryurko)This patch release of workflowr includes minor improvements, updated documentation, bug fixes, and lots of internal refactoring.
Workflowr functions check if the working directory exists (idea from @pcarbo, #185)
wflow_use_github() can now create repositories for GitHub organizations using the new argument organization. However, GitLab Groups should still be specified with the argument username for wflow_use_gitlab() (bug report from @stephens999, #186)
Any workflowr function that prompts for user input will continue to re-prompt until valid input has been entered (or canceled by hitting the key Esc) (idea from @pcarbo)
All functions that commit to the Git repository first check for the availability of the Git variables user.name and user.email (either global or local), which are required for creating a commit (#85)
The workflowr icon is displayed in browser tabs of workflowr websites (idea from @pcarbo)
Document that GitLab.com provides private repositories with access control to the source code repository and the website (#187)
Update URL to RStudio-specific instructions for installing pandoc (bug report from @PietrH, #190)
Document in the FAQ vignette how to include an external image using an absolute URL to the image hosted on another website (idea from @JiaxiangBU, #159)
Document how to embed Shiny apps with knitr::include_app() and shinyapps.io (idea from @rsimon64, #130)
Update the FAQ on including external images to account for the breaking change in knitr::include_graphics() introduced in knitr version 1.28 (bug report from @ditordccaa, #103)
Add FAQ entry on how to use a Git hosting site that uses the HTTP protocol (idea from @antass, #163)
Internal refactoring for increased speed and improved error handling of input arguments
Check for class with inherits() (#189)
Switch to use pandoc option --include-in-header to insert workflowr-specific CSS and other metadata (surprisingly --include-before-body works fine)
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
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.
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")
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().
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.
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:
workflowr:
suppress_report: TRUE
Many thanks to @kaneplusplus for implementing this feature! (#168)
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.
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 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 >=1.3.0
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.
This minor release of workflowr features further GitHub integration, a new reproducibility check, and various improvements and bug fixes.
The initial GitHub setup always included the manual step of creating the
GitHub repository, but this is no longer the case! When you run
wflow_use_github("username"), it will offer to create the new GitHub
repository for you. If you sign-in to GitHub via your web browser and grant
workflowr permission, it will be created automatically.
Absolute paths to files on your local computer are not reproducible. If you or someone else tries to execute the code on a different machine, it will fail. Now workflowr will automatically search for absolute paths to files that are inside of the workflowr project. If it detects any, it will fail the reproducibility check, and provide you with the equivalent relative paths to use.
Now every time you push your latest changes with wflow_git_push(), a new
browser tab will automatically be opened to your online repository
(idea from @pcarbo)
knitr::include_graphics() as an option for including external images
(idea from @Zepeng-Mu, #162)wflow_build() and wflow_publish() build the files in the
given order if they are provided explicitly to the argument files (idea from
@antass and @pcarbo, #164)wflow_use_github()/wflow_use_gitlab() provide better guesses if the
arguments username or repository are left blank. If repository is NULL,
it is set to the name of the workflowr project directory (idea from @pcarbo).wflow_git_push() and wflow_git_pull() no longer accept direct URLs to
remote repositories. The argument remote must be NULL or the name of an
existing remote. The support for direct URLs was likely rarely used since it is
rarely used with Git as well, and it likely never worked given how the
underlying functions from git2r work.wflow_git_push() (this is
a feature unique to GitLab)This minor release of workflowr introduces two new functions, RStudio Addins, and various minor improvements.
The new function wflow_toc() builds a table of contents of the published R
Markdown files in a workflowr project (@JiaxiangBU, #151, #155)
The new function wflow_rename_proj() renames a workflowr project throughout
all its project files (idea from @frm1789 and @kbroman, #148)
RStudio Addins allow you to execute R code via the RStudio Addins menu. For extra convenience, you can bind the addins to keyboard shortcuts. The following workflowr functions have addins:
wflow_build()
wflow_publish()
wflow_status()
wflow_toc()
wflow_view()
Note that the addin for wflow_publish() is a Shiny Gadget that enables you to
interactively choose which files to publish and write a detailed commit message
(assistance from @zaynaib and @argdata, #143).
wflow_build() fails early if pandoc is not installed (@zaynaib, #75)
wflow_git_push()/wflow_git_pull() fail early if user tries to use SSH
authentication when it is not supported by the current installation of
git2r/libgit2 (#144)
Fix support for knitr chunk option collapse and indent (reported by
@pcarbo, #149)
Fix support for rmarkdown option keep_md (see
rmarkdown Issue 1558)
Skip tests that only fail on CRAN servers (this is why there are no macOS binaries for 1.2.0)
Add a GitHub Pull Request template
Rename reproducibility tab "Report" to "Checks" (idea from @pcarbo)
Fix spacing issue with session information button (reported by @pcarbo, #157)
wflow_status() reports if the configuration files _workflowr.yml and
_site.yml have been edited
Disable inline code chunks by default in R Markdown files created by workflowr. Document how to use inline code chunks in the FAQ (discussed with @rgayler and @Robinlovelace , #140)
This release overhauls the layout of the reproducibility report, adds support for GitLab, introduces some safety checks and warnings related to caching, provides more documentation, and more.
While it has always been possible to host workflowr projects using platforms other than GitHub, it was less convenient and not all the features were supported. With this release, a workflowr project hosted on GitLab has all the same features as a workflowr project hosted on GitHub, including links to past versions of the R Markdown, HTML, and figure files. It's also possible to use workflowr with GitHub Enterprise or a custom GitLab instance, but you'll have to coordinate with your administrators to make sure it's possible to host the website.
domain to wflow_git_remote() to allow specifying any remote
Git host, e.g. domain = "gitlab.com"
wflow_use_gitlab() to automate GitLab setupThe layout of the reproducibility report and other content that workflowr inserts in the HTML output has been overhauled to be both highly informative but also collapsed by default. This way the information is there if you need it, but otherwise is minimally distracting.
wflow_use_github() or wflow_use_gitlab() to
insert a link to your workflowr project into the navigation barA popular knitr/rmarkdown feature is caching slow-running chunks. This can be
problematic for workflowr because it assumes that the results are newly created
when wflow_publish() publishes the results with a given version of the code.
In this release, workflowr now provides warnings, safety checks, and some
convience arguments for safely using caching.
cache=TRUE) but is not set to re-run if its upstream chunks are
changed (autodep=FALSE)clean_fig_files to wflow_build(). The default for
wflow_build() is FALSE, so that old figures are not removed. This is useful
for iterative development when plots from cached chunks may not be regenerated
during a build. However, clean_fig_files is fixed to TRUE for
wflow_publish() to ensure that the final results are produced during the
build (suggested by @lazappi, #113)delete_cache to wflow_build()/wflow_publish(). The defult
is FALSE, but if set to TRUE it will delete the cache directory prior to
building each R Markdown file. This helps ensure reproducibility of the
published resultswflow_build() send message about status of cache directoryIn addition to the new vignette on GitLab, this release has multiple other new vignettes plus updates to existing ones.
wflow_use_github()
fig_path_ext: false in _workflowr.yml removes the file extension from the
figure subdirectories, allowing them to be viewed on Shiny Server (implemented
by @Tutuchan, #119, #122)fig.path, which workflowr ignores (idea from @lazappi, #114)disable_remote to wflow_start(). It creates a Git pre-push
hook that disables the ability to push to a remote repository.
Useful for confidential projects. Currently only available for Linux and macOS
(suggested by @rgayler, #141)wflow_html() to facilitate
integrating workflowr features into other R Markdown output formats such as
blogdown (suggested by @docmanny, #126)wflow_rename() to rename files and directories, including
committing the change with Gitwflow_publish()/wflow_git_commit() fail early if any of the files
have merge conflictswflow_git_push() set the upstream tracking branch by default (see
git2r Issue 375)wflow_build() report the current working directory. If the knit
directory (where the code is executed) is different than the working directory,
have wflow_build() report where the code in each file is being executedFix unit test on CRAN Windows servers.
See the release notes for v1.1.0 for the recent changes.