Skip to content

Latest commit

 

History

History
684 lines (505 loc) · 29.4 KB

NEWS.md

File metadata and controls

684 lines (505 loc) · 29.4 KB
Raw

workflowr 1.4.0.9000

  • Require git2r >= 0.26.0 to support internal changes that increase speed and robustness of workflowr Git functionality.

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 with wflow_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() 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)
  • 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 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.
  • Document in the GitLab vignette that the repository will be automatically created the first time the repository is pushed with wflow_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 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).

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 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)

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() or wflow_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 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)
  • Add argument delete_cache to wflow_build()/wflow_publish(). The default 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 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 function wflow_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 option 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)
  • Insert warning into HTML if user configures the knitr chunk option fig.path, which workflowr ignores (idea from @lazappi, #114)
  • Add argument 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)
  • Refactor and export the individual functions of wflow_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 function wflow_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 to wflow_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 to wflow_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() if getOption("browser") does not provide a default option

Internal changes

  • Dramatically increase speed of wflow_status()/wflow_publish() by using git2r::odb_blobs() to obtain past commit times of files (if these functions are still slow for you, try running git gc in 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 file analysis/.nojekyll (related to point above). Unlike rmarkdown:::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 if wflow_publish() fails to build any of the files (reported by @pcarbo)

  • If a user has not set the Git configuration variables user.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 that wflow_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.R with the output format wflow_html() and site generator wflow_site(). This enables a much more informative reproducibility report to be created.

# Install from GitHub
devtools::install_github("jdblischak/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() and wflow_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 via wflow_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 like wflow_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 with devtools::install_version("git2r", "0.21.0") and then retry installing workflowr. If your machine is running macOS or Windows, you may need to run install_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() or wflow_git_pull() fails for an unknown reason, the exact error message from git2r::push() or git2r::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 thus wflow_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 with wflow_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 globs as 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 runs render_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 options user.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 run wflow_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 to git 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() and wflow_status() are introduced, and the previous functions wflow_build() and wflow_commit() are re-designed.

wflow_status

  • New function wflow_status() reports which analysis files require user attention (inspired by git 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 of wflow_commit(). The basic interface is much simpler.

  • wflow_publish("analysis/file.Rmd") will 1) commit analysis/file.Rmd, 2) build analysis/file.Rmd in 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 file analysis/_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 and git 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 of git 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 with project to clarify that this argument specifies the path to a directory in the workflowr project

  • wflow_start() now includes docs/.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 (set standalone = 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

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.