NEWS.md

In jdblischak/workflowrBeta: A workflow template for creating a research website

workflowr 0.12.0

Create separate repository workflowrBeta for early adopters to continue using beta version of workflowr for existing projects. New users are encouraged to the latest workflowr release.

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 faciliate 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 mutliple 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 Browswer (@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 specfically 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 extesion .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

• Continuous integration testing with Travis CI
• Code coverage with covr and 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 commiting 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.

jdblischak/workflowrBeta documentation built on May 17, 2019, 7:28 p.m.