NEWS (original) (raw)

workflowr 1.7.1

This patch release includes improved documentation, bug fixes, and a reduction in the number of Suggested dependencies.

Updated documentation

• 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 to the package overview help file as per “Documenting packages” in Writing R Extensions
• Modernize CITATION. Replace citEntry()with bibentry(), replace personList() withc(), format as R code, and simplify.

Bug fixes

• 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() inprint.wflow_start() when git = FALSE

Dependencies

• Removed from Imports: xfun
• Removed from Suggests: covr, devtools, spelling
• Added to Suggests: sessioninfo

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 likemake = 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 ranwflow_build("analysis/example*.Rmd", make = TRUE, combine = "and"), then this would only build those Rmd files matched by the file globanalysis/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 orupdate = 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 argumentmessage 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 --onelinesince these only show the title (suggestion from @LearnUseZone in #222, implementation by @zaynaib in #225)
• New argument only_published forwflow_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 .Rprofilefile (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 threadfor more details
• Bug fix: wflow_use_github() andwflow_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 withbase_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)

workflowr 1.6.2

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).

Minor improvements

• Make the HTTP calls by wflow_use_github() to the GitHub API more resilient to transient network issues by automatically retrying HTTP calls more than once (@jameslamb, #199, #201)
• Enhance the RStudio Project Template to include more arguments fromwflow_start() (@trannhatanh89, #193, #200)
• Throw error early if user sets overwrite = TRUE towflow_start() but existing = FALSE, since it isn’t possible to overwrite non-existent files (@skpurdue, #194, #202, idea from @pcarbo)

Updated documentation

• Update FAQ entry on external images to note that the website directory for GitLab Pages is public/, notdocs/ (idea from @ryurko)

Bug fixes

• Send warning if Python plots created using outdated version of reticulate (< 1.15) (bug report from @lazappi, #181)
• Make workflowr compatible with fs version 1.4.1.9000+ (@jimhester, #204)
• Set minimum version requirement for dependency rprojroot to 1.2
• Skip test of error handling of deleted working directory on Solaris

workflowr 1.6.1

This patch release of workflowr includes minor improvements, updated documentation, bug fixes, and lots of internal refactoring.

Minor improvements

• 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 argumentusername 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)

Updated documentation

• 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 withknitr::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)

Bug fixes

• Fix Windows-specific bug that caused the table of past versions to be missing from the workflowr report (bug introduced in version 1.5.0)

Internal refactoring

• 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)

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 functionswflow_build(), wflow_publish(), andwflow_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 optionworkflowr.autosave to FALSE (idea from @xiangzhu in #179)
• New vignetteon using large data files in a workflowr project (motivated by @xiangzhu, #183)
• If there are merge conflicts after runningwflow_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 argumentoverwrite. Previously wflow_git_config() would by default overwrite any previous settings. Now this will throw an error. To overwrite a previous setting, setoverwrite = TRUE (ideafrom @petebaker)

Minor improvements and bug fixes

• 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 ofwflow_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 orgit pull in the terminal if eitherwflow_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

workflowr 1.5.0

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 functionoptions()) 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 is TRUE only if it is an interactive R session). This option is currently used bywflow_build(), wflow_git_push(), andwflow_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 toTRUE. 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 fixes

• Require git2r >= 0.26.0 to support internal changes that increase speed and robustness of workflowr Git functionality
• wflow_start() adds a .gitattributesfile 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 fileindex.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 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 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 thatwflow_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.

workflowr 1.4.0

This minor release of workflowr features further GitHub integration, a new reproducibility check, and various improvements and bug fixes.

New features

• 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 withwflow_git_push(), a new browser tab will automatically be opened to your online repository (idea from @pcarbo)

Minor improvements and bug fixes

• Mention knitr::include_graphics() as an option for including external images (idea from @Zepeng-Mu, #162)
• Check if Git repository is locked and produce error message that explains how to fix it (idea from @brimittleman)
• Document that wflow_build() andwflow_publish() build the files in the given order if they are provided explicitly to the argument files (idea from@antass and @pcarbo, #164)
• Handle spaces in chunk names for HTML targets. If a chunk name contains a space, the name of the figure file will also has a space. This broke the accompanying link for the HTML button with the table of previous versions of the figure (because it uses the filename to be unique). Now the spaces are removed in the HTML link.
• Add FAQ entry on installing packages in a workflowr project (idea from @xiangzhu, #160)
• wflow_use_github()/wflow_use_gitlab()provide better guesses if the arguments username orrepository are left blank. If repository isNULL, 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 argumentremote 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.
• Document in the GitLab vignette that the repository will be automatically created the first time the repository is pushed withwflow_git_push() (this is a feature unique to GitLab)

workflowr 1.3.0

This minor release of workflowr introduces two new functions, RStudio Addins, and various minor improvements.

New functions

• 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

RStudio Addinsallow 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).

Minor improvements and bug fixes

• 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 andindent (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)

workflowr 1.2.0

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.

Full support for GitLab

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.

• Create vignette “Hosting workflowr websites using GitLab” (written with @lazappi, #112)
• Add argument domain to wflow_git_remote()to allow specifying any remote Git host, e.g. domain = "gitlab.com"
• Create function wflow_use_gitlab() to automate GitLab setup

Reproducibility report and other layout changes

The 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.

• Collapse the reproducibility report (suggested by @timtrice, #110)
• Collapse the “Session information” chunk (suggested by @xiangzhu, #120)
• Convert table of past figure versions to a collapsable button (suggested by @xiangzhu, #120)
• Improve formatting of tables of past version of files using Bootstrap table classes
• Remove the footer
• Report the knit directory (where the code was executed) in the workflowr report
• Link to workflowr GitHub repository no longer automatically inserted into navigation bar. Use either wflow_use_github() orwflow_use_gitlab() to insert a link to your workflowr project into the navigation bar

Improved support for caching

A 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 convenience arguments for safely using caching.

• Include a check in the reproducibility report that reports any existing cached chunks
• A warning is inserted directly in the HTML file after any code chunk that is cached (cache=TRUE) but is not set to re-run if its upstream chunks are changed (autodep=FALSE)
• Add argument clean_fig_files towflow_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)
• Add argument delete_cache towflow_build()/wflow_publish(). The default isFALSE, 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 results
• Have wflow_build() send message about status of cache directory

Documentation

In addition to the new vignette on GitLab, this release has multiple other new vignettes plus updates to existing ones.

• Add vignette “Sharing common code across analyses” (written with@timtrice, #111, #142)
• Add vignette “Alternative strategies for deploying workflowr websites”
  • Password-protected site with Amazon S3 (written by @edavidaja, #124)
  • Secure sharing with Beaker Browser (written by @johnsonlab, #59, #65)
• Update getting started vignette to use new functionwflow_use_github()
• Add section “Style with custom CSS” to customization vignette
• Add FAQ entry “How can I include external images in my website?”
• Add code of conduct

Miscellaneous

• Improve support for hosting on Shiny Server. Setting the optionfig_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)
• Insert warning into HTML if user configures the knitr chunk optionfig.path, which workflowr ignores (idea from @lazappi, #114)
• Add argument disable_remote towflow_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)
• Refactor and export the individual functions ofwflow_html() to facilitate integrating workflowr features into other R Markdown output formats such as blogdown (suggested by@docmanny, #126)
• New function wflow_rename() to rename files and directories, including committing the change with Git
• Use fs internally to improve cross-platform handling of file paths
• Have wflow_publish()/wflow_git_commit()fail early if any of the files have merge conflicts
• Switch from rawgit to raw.githack to serve past versions of HTML files (#134)
• Have wflow_git_push() set the upstream tracking branch by default (see git2r Issue 375)
• Have 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 executed
• As usual, some minor bug fixes, improved error handling, and more tests

workflowr 1.1.1

Fix unit test on CRAN Windows servers.

workflowr 1.1.0

workflowr 1.1.0 is a maintenance release. It includes some minor new features, improved error handling, and bug fixes. Critically, it makes workflowr compatible with the latest release of git2r.

The most noticeable changes are 1)wflow_publish()/wflow_status() are now much faster, especially if your project has many R Markdown files and/or many Git commits, 2) the rmarkdown package is no longer loaded automatically when you load workflowr, and 3) the new functionwflow_open() (based on a previous version in workflowrBeta) to open new or existing R Markdown files.

New features

• Resurrect wflow_open(). Since there is no longer a workflowr template in workflowr 1.0+, it creates a file with a minimal YAML header (@xiangzhu, #107)
• Add bibliography before session information (reported by @docmanny, #102)
• Add argument verbose towflow_build()/wflow_publish() to display the build log in the R console as each file is built. Useful for monitoring long-running code chunks (idea from @pcarbo)
• Argument dry_run added towflow_start()
• S3 print method for wflow_start()
• Updates to wflow_view():
  • Renamed argument recent to latest to display the most recently modified HTML file
  • The argument files now requires correct paths to existing R Markdown or HTML files. Previously, wflow_view()would guess the correct path. While convenient, it was also potentially confusing since it was inconsistent with the other workflowr functions
  • The argument latest is no longer mutually-exclusive with files. If the most recently modified HTML is different than those specified by files, they will all be opened for viewing
  • S3 print method
  • Do not attempt to open HTML files with browseURL() ifgetOption("browser") does not provide a default option

Internal changes

• Dramatically increase speed ofwflow_status()/wflow_publish() by usinggit2r::odb_blobs() to obtain past commit times of files (if these functions are still slow for you, try running git gcin the Terminal)
• Make workflowr compatible with latest release of git2r as well as previous versions
• Move rmarkdown from Depends to Imports. Unlike earlier versions, it’s no longer necessary to call rmarkdown functions directly when using workflowr (which was the original intention of attaching rmarkdown). Also there is the potential for problems to arise from the order in which packages are loaded in a user’s R session (described here)
• Remove the fields include/exclude from the template _site.yml. Also remove the fileanalysis/.nojekyll (related to point above). Unlikermarkdown:::default_site, wflow_site() does not copy the entire directory to the output directory, so these fields have no effect. See the R Markdown documentation on Included files for more information
• Add GitHub Issue Templates (created by @pcarbo)

Bug fixes and improved error handling

• Fix Windows-specific bug in wflow_publish(),wflow_remove(), and wflow_git_commit(). The bug prevented Windows users from running these functions from a subdirectory of a workflowr project
• Restore all files in website directory ifwflow_publish() fails to build any of the files (reported by @pcarbo)
• If a user has not set the Git configuration variablesuser.name and user.email, any workflowr function that creates a Git commit will throw an informative error message. Previously this was only done for wflow_start(), but has been expanded to wflow_git_commit(),wflow_publish(), and wflow_remove() (idea from@pcarbo)
• Ensure that wflow_build() creates a new.nojekyll file if necessary and thatwflow_publish() commits it. This is most useful when changing the name of the output directory (#72)

workflowr 1.0.1

Various minor changes to documentation, tests, and package infrastructure to prepare for CRAN submission.

workflowr 1.0.0

The 1.0.0 release is a major change. Instead of relying on the external code chunks in chunks.R to implement the reproducibility features, workflowr 1.0.0 replaces chunks.Rwith the output format wflow_html() and site generatorwflow_site(). This enables a much more informative reproducibility report to be created.

# Install from GitHub
devtools::install_github("workflowr/workflowr")

# Start a new project to test out the new features
wflow_start("testproject")

# Learn about the new ways to customize your site
?wflow_html

# Update an existing project
wflow_update()

Details

• Introduce wflow_html() and wflow_site() to overhaul the reproducibility features of workflowr
• Improve API consistency:
  • wflow_commit() ->wflow_git_commit()
  • wflow_remotes() ->wflow_git_remote()
• Remove some less commonly used infrastructure files
• Remove template infrastructure: wflow_open() andwflow_convert()
• Reimplement wflow_update() to update a pre-1.0 workflowr project to a post-1.0 project
• Remove create_links_page() (not widely used, if at all)
• Note in documentation that setting the seed viawflow_build() or wflow_publish() is ignored if using wflow_html()
• wflow_publish(republish = TRUE) does not build HTML files that have unstaged/staged changes
• wflow_build() reports the total number of files that will be built
• Enable wflow_start() to set local Git user.name and user.email. Preferred method for most users is still to set global Git user.name and user.email with wflow_git_config().

workflowr 0.11.0

• wflow_publish() now views the website by default if run interactively (view = interactive()) just likewflow_build()
• Pin the dependency git2r to version 0.21.0 or lower because of the forthcoming breaking changes in the git2r API. This is not a great solution because install.packages() always installs the latest version, which will cause an error in the installation. If you are having trouble with this, first install git2r withdevtools::install_version("git2r", "0.21.0") and then retry installing workflowr. If your machine is running macOS or Windows, you may need to runinstall_version("git2r", "0.21.0", type = "binary").
• Fix minor bug that affected the error message produced for a failed push or pull using the SSH protocol
• When wflow_git_push() orwflow_git_pull() fails for an unknown reason, the exact error message from git2r::push() orgit2r::pull() is reported to facilitate troubleshooting
• Multiple other internal changes to make workflowr more robust

workflowr 0.10.2

Fix bug that caused wflow_status() (and thuswflow_publish()) to ignore R Markdown files with the all lowercase file extension .rmd (reported by @LSun and @pcarbo). This was recently introduced in commit a8ce711, so it only affected versions 0.10.0 and 0.10.1.

workflowr 0.10.1

Fix bug that prevented deleted files from being committed withwflow_commit() or wflow_publish() (reported by@pcarbo)

workflowr 0.10.0

Integration with RStudio Viewer

• wflow_view() (or wflow_build()) now opens the website in the RStudio Viewer if run from within RStudio

File globbing

• Main workflowr functions now accept file globsas input (#84)

Miscellaneous

• wflow_build() automatically removes unused figure files
• Improved documentation of wflow_build() arguments

workflowr 0.9.0

New RStudio project template

• New workflowr projects can now be created directly in RStudio using the workflowr project template (requires RStudio v1.1.28 or greater)

Improved support for Windows

• Implemented continuous integration testing for Windows with AppVeyor
• Fixed unit test failures due to edge cases in Windows (#76)
• Skip evaluation of vignette code during installation if the machine does not have the necessary configuration (#87, #88)

Log files

• The log files by default are now written to the directory returned by tempdir() instead of to /tmp/workflowr. This prevents failures due to permission issues when multiple workflowr users try to use the same machine (e.g. a compute node on a HPC cluster) (#86)

Miscellaneous

• Bug fix: When using wflow_build() to build the R Markdown files in an external R process, it now runsrender_site() in the global environment of the external R process. This better mimics the results of the RStudio “Knit” button.

workflowr 0.8.0

Git installation is now optional

• It is no longer required to install Git prior to using workflowr. Git can be installed at a later time if more advanced operations are needed. The Quick Start and Getting Started vignette have been updated to reflect this.
• wflow_git_config() sets the Git optionsuser.name and user.email
• wflow_git_push() pushes changes from the local computer to GitHub
• wflow_git_pull() pulls the changes from GitHub to the local computer

Miscellaneous

• Added FAQ on sharing workflowr sites securely using Beaker Browser (@johnsonlab in #59 & #65)
• Added .Rprofile to automatically load workflowr (@vanAmsterdam in #73)
• Added FAQ about website not displaying (#70)
• Added tag to footer.html to adjust MathJax settings so that all math formulae are shown using TeX fonts only. This will make the presentation more consistent at the cost of the webpage sometimes taking slightly longer to load. (@pcarbo)
• Increase spacing between sections in HTML (@pcarbo in #57)
• Minor changes to improve error messages (#61)
• Minor updates to documentation

workflowr 0.7.0

wflow_build

• wflow_build() automatically opens the website after building files, thus it’s not necessary to always runwflow_view() manually afterwards. If one file is built, then that file is opened. If more than one file is built, then the index page is opened. (#41)
• wflow_build() adds objects to the global environment when building files locally in the R console (i.e. local = TRUE) (#53)

Miscellaneous

• Bug fix so workflowr can process Emacs backup files that contain a tilde (#47)
• Bug fix so print methods display properly in the R console (some did not end with a newline character)

workflowr 0.6.0

New function wflow_remove

• wflow_remove() removes R Markdown files and all their associated files (e.g. HTML and figures)
• If the files to be removed had been committed to the Git repository, the files are also removed from the Git repository (analogous togit rm)
• wflow_remove() also works on non-Rmd files

Improved support for Windows

• workflowr functions can now handle backslashes in filepaths
• wflow_update() and wflow_convert() fail gracefully if the diff utility is not available and inform the user to install Rtools

Miscellaneous

• Added continuous integration testing with Travis CI for macOS
• Updated documentation in README, “Getting started” vignette, and FAQ

workflowr 0.5.1

This minor release fixes a bug in how filepaths are resolved so that workflowr can run on Windows.

workflowr 0.5.0

This release changes the interface of some of the main workflowr functions. The functions wflow_publish() andwflow_status() are introduced, and the previous functionswflow_build() and wflow_commit() are re-designed.

wflow_status

• New function wflow_status() reports which analysis files require user attention (inspired bygit status)
• Defines R Markdown files whose HTML has been committed as part of the Git repo as “Published”, R Markdown files which have been committed to the Git repo but not their HTML as “Unpublished”, and R Markdown files that are untracked by Git as “Scratch”. Furthermore, previously published files that have been subsequently edited are classified as “Modified”. See the man page ?wflow_status for more details.

wflow_publish

• This new function replaces the previous functionality ofwflow_commit(). The basic interface is much simpler.
• wflow_publish("analysis/file.Rmd") will 1) commitanalysis/file.Rmd, 2) build analysis/file.Rmdin its own separate R session with set.seed(12345), and 3) commit docs/file.html and any generated figures. These 3 steps are referred to as “publishing a file”.
• wflow_publish(all = TRUE) will publish all tracked analysis files, analogous to git commit -a.
• To change the theme or make some other change to the entire site, run wflow_publish("analysis/_site.yml", republish = TRUE), which will 1) commit the configuration fileanalysis/_site.yml, 2) re-build all the previously published analysis files using the new configuration options, and 3) commit the re-built HTML files.

wflow_build

• By default, wflow_build() runs in “Make”-mode, only building R Markdown files that have been updated more recently than their corresponding HTML files. If instead files are specifically stated, those files will be built.
• By default, R Markdown files are now built each in their own separate R session (similar in function to the “Knit HTML” button in RStudio). This prevents undesirable behavior like sharing variables and loaded packages across separate files. Set local = TRUE to build the files in the local R console (useful for debugging, but otherwise discouraged).
• By default, the seed for random number generation is set to the arbitrary number 12345 (using set.seed()). This ensures that any code that produces random numbers will be reproducible.

wflow_commit

• wflow_commit() has been demoted to only being a wrapper for the equivalent functionality of git add andgit commit. This can be useful for committing non-analysis files or R Markdown files that you aren’t ready to publish yet. However, you should use wflow_publish() for the standard workflow.
• Set all = TRUE to run the equivalent ofgit commit -a.

wflow_update

• Improved documentation of wflow_update() to better explain its functionality. It will attempt to convert all R Markdown files present to use the latest version of the workflowr R Markdown template; however, it will only commit R Markdown files that are tracked by Git.

Miscellaneous

• All workflowr functions should now accept the file extension.rmd in addition to .Rmd (Issue #10)
• Replaced the shared argument path withproject to clarify that this argument specifies the path to a directory in the workflowr project
• wflow_start() now includesdocs/.nojekyll
• Change dependency to R >= 3.2.5 (Issue #32)
• Change stringr dependency (>= 1.1.0)
• Started a vignette with Frequently Asked Questions
• Added sections to README (Quick start, Upgrading, Related work, and Citation)

workflowr 0.4.0

wflow_start

• The wflow_start() API has been simplified. Now the first (and only required) argument is the directory to be created. By default, the name of the project will be determined from the directory name. For example, wflow_start("~/projects/proj-x") will create a workflowr project with the name “proj-x”. To specify a different name, provide the argument name
• New argument change_wd = TRUE changes the working directory to the newly created project.
• New argument existing = FALSE is a safety feature so that by default workflowr projects are only created in new directories
• wflow_start() no longer adds “BuildType: Website” to RStudio project file. Users should run wflow_build()instead. wflow_update() removes the build specification for existing workflowr projects
• Fixed bugs related to relative paths and nested paths

workflowr R Markdown template

• Updated workflowr R Markdown template can be built even if the user does not have workflowr installed
• Use new function wflow_convert() to convert an R Markdown file based on the previous template to use the latest version
• New optional “standalone” version of the workflowr template for creating files outside of a workflowr project (setstandalone = TRUE for wflow_open())
• Can create a workflowr R Markdown file outside of a workflowr project by setting path = NULL

Migrating an existing project to use workflowr

• New vignette on “Migrating an existing project to use workflowr”
• wflow_update() function updates workflowr projects to use the latest version of the template
• wflow_convert() converts an existing R Markdown file to use the workflowr template (can also update a file that uses a previous version of the template)

Other new functions

• wflow_view() opens the website in the browser
• wflow_remotes() manages remote Git repositories on GitHub. It can add a remote, remove a remote, or update the URL for an existing remote

Improvements to the workflowr R package itself

• Continuous integration testing with Travis CI
• Code coverage with covrand Codecov
• Package documentation with pkgdown

workflowr 0.3.0

• Second alpha release. Major API overhaul.
• Improved naming of functions: start_project ->wflow_start, open_rmd ->wflow_open, build_site ->wflow_build, commit_site ->wflow_commit, create_results ->create_links_page
• wflow_commit can optionally add and commit provided files (argument is commit_files) before re-building website and committing HTML files
• wflow_open accepts multiple filenames
• Both wflow_build and wflow_commit have the argument all to optionally build all the HTML files

workflowr 0.2.0

• First alpha release. Contains enough functions to create workflowr project from scratch.
• Main functions: start_project,open_rmd, build_site,commit_site, create_results

workflowr 0.1.0

• Initial demonstration of idea.