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 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: TRUETo suppress the report in a specific HTML file, add the following to the YAML header of the corresponding Rmd file:
workflowr:
suppress_report: TRUEMany 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 convenience 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 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 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.
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.
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)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)dry_run added to
wflow_start()wflow_start()wflow_view():
recent to latest to
display the most recently modified HTML filefiles 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
functionslatest 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
viewingbrowseURL() if
getOption("browser") does not provide a default optionwflow_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)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 informationFix 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)
Various minor changes to documentation, tests, and package infrastructure to prepare for CRAN submission.
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("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()wflow_html() and wflow_site() to
overhaul the reproducibility features of workflowrwflow_commit() ->
wflow_git_commit()wflow_remotes() ->
wflow_git_remote()wflow_open() and
wflow_convert()wflow_update() to update a pre-1.0
workflowr project to a post-1.0 projectcreate_links_page() (not widely used, if at
all)wflow_build() or wflow_publish() is ignored if
using wflow_html()wflow_publish(republish = TRUE) does not build HTML
files that have unstaged/staged changeswflow_build() reports the total number of files that
will be builtwflow_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().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
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.
Fix bug that prevented deleted files from being committed with
wflow_commit() or wflow_publish() (reported by
@pcarbo)
wflow_view() (or wflow_build()) now opens
the website in the RStudio
Viewer if run from within RStudiowflow_build() automatically removes unused figure
fileswflow_build() argumentstempdir() 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)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.wflow_git_config() sets the Git options
user.name and user.emailwflow_git_push() pushes changes from the local computer
to GitHubwflow_git_pull() pulls the changes from GitHub to the
local computerwflow_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)wflow_remove() removes R Markdown files and all their
associated files (e.g. HTML and figures)git rm)wflow_remove() also works on non-Rmd fileswflow_update() and wflow_convert() fail
gracefully if the diff utility is not available and inform
the user to install RtoolsThis minor release fixes a bug in how filepaths are resolved so that workflowr can run on Windows.
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.
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.
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.
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() 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() 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.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)
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 namechange_wd = TRUE changes the working
directory to the newly created project.existing = FALSE is a safety feature so
that by default workflowr projects are only created in new
directorieswflow_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 projectswflow_convert() to convert an R
Markdown file based on the previous template to use the latest
versionstandalone = TRUE for wflow_open())path = NULLwflow_update() function updates workflowr projects to
use the latest version of the templatewflow_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)wflow_view() opens the website in the browserwflow_remotes() manages remote Git repositories on
GitHub. It can add a remote, remove a remote, or update the URL for an
existing remoteSecond 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
First alpha release. Contains enough functions to create workflowr project from scratch.
Main functions: start_project,
open_rmd, build_site,
commit_site, create_results