The Dovetail #4: Updates from The Carpentries Workbench

This is the fourth post in a series that we are calling “The Dovetail.” In this series, we aim to keep members of The Carpentries community abreast of the current news for The Carpentries Workbench.

If you are interested in participating in discussions around The Carpentries Workbench, head over to our GitHub Discussions forum: https://github.com/carpentries/workbench/discussions

Announcements

For anyone who has questions about The Workbench, I will be hosting two themed community discussions:

• (UTC) Friday 08 July 2022 14:00 (find your time)
• (UTC) Tuesday 12 July 2022 00:00 (find your time)

Updates to The Carpentries Workbench

Since 2022-06-08,

• {sandpaper} version 0.6.0 -> 0.7.1
  • Creating a new lesson from the R package now defaults to an Incubator lesson.
  • If you have a lesson that uses R Markdown and want unexpected errors to cause build failures, place fail_on_error: true in your lesson’s config.yaml file.
• {varnish} version 0.1.14 -> 0.2.0
  • Sidebar navigation on mobile and tablet views now includes all the information that was included in the navigation bar for desktop mode.
• {pegboard} (no updates)

To update your local Workbench installation, open R and use the following code:

# Enable repository from carpentries
options(repos = c(
  ropensci = 'https://carpentries.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))
# Download and install sandpaper in R
install.packages(c('tinkr', 'pegboard', 'sandpaper', 'varnish'))

Upcoming and Current Lessons in Workbench Beta

List of Lessons to enter Workbench Beta in 2022

By this time next week, datacarpentry/R-ecology-lesson—Data Analysis and Visualization in R for Ecologists (✅ approved by maintainers) will enter Workbench Pre-Beta which means that a snapshot of the lesson will be available at https://lessons.datacarpentry.org/R-ecology-lesson (note: there is no page here yet).

Official Lessons

• datacarpentry/R-ecology-lesson—Data Analysis and Visualization in R for Ecologists (✅ approved by maintainers)
• datacarpentry/r-socialsci—R for Social Scientists (✅ approved by maintainer)
• datacarpentry/r-raster-vector-geospatial—Introduction to Geospatial Raster and Vector Data with R (⏳ awaiting responses)
• datacarpentry/OpenRefine-ecology-lesson—Data Cleaning with OpenRefine for Ecologists (✅ approved by maintainer)
• librarycarpentry/lc-shell—Library Carpentry: The UNIX Shell (⏳ awaiting responses)
• carpentries/instructor-training—Instructor Training (⏳ awaiting responses)

Tentative schedule for official lessons

Community Lessons

• carpentries-incubator/git-novice-branch-pr—Version Control with Git
• carpentries-incubator/data-management-pipelines-engineering—Data management and analytic pipelines for engineers
• carpentries-incubator/markdown-intro—Introduction to Markdown
• carpentries-incubator/SDC-BIDS-IntroMRI—Introduction to MRI and BIDS
• carpentries-incubator/SDC-BIDS-dMRI—Introduction to dMRI
• carpentries-incubator/SDC-BIDS-fMRI—fMRI Imaging Analysis
• carpentries-incubator/julia-novice—A lesson exploring the Julia language
• carpentries-incubator/R-archaeology-lesson
• carpentries-incubator/python-packaging-publishing—Packaging and Publishing with Python

Participants

• Eirini Zormpa, Maintainer
• James Sadler, Maintainer
• Robin, Instructor
• Jon Haitz Legarreta Gorroño, Lesson Developer (in The Carpentries Incubator)
• Karen Word, Maintainer
• Luis J. Villanueva, Maintainer
• Jon Wheeler, Lesson Developer (in The Carpentries Incubator)
• Simon Christ, Lesson Developer (in The Carpentries Incubator)
• Maneesha Sane, Instructor
• Sarah Brown, Maintainer
• Joel Nitta, Translator
• Juan Fung, Maintainer
• Jannetta Steyn, Lesson Developer (in The Carpentries Incubator)
• Michael Joseph, Lesson Developer (in The Carpentries Incubator)
• Sarah Stevens, Lesson Developer (in The Carpentries Incubator)
• Kozo Nishida, Lesson Translation (to Japanese)
• François Michonneau, Maintainer
• Jamie Jamison, Maintainer
• Jennifer Stubbs (she/her), Instructor
• Drake Asberry, Maintainer

Updates from Community About Working in Workbench Beta

Tips and Tricks for Using The Workbench

If you maintain a lesson on The Carpentries Infrastructure, you get the following Automated pull requests that help you ensure your lesson stays up-to-date and healthy:

1. A weekly pull request that checks for updates to GitHub Workflows
2. (for R-based lessons) a monthly pull request that updates the versions of packages used in the lesson

Both of these pull requests are issued by @carpentries-bot, but if you are not a member of a Carpentries organisation, then you will not get these pull requests, but you can still update locally with the following {sandpaper} calls:

library("sandpaper")
update_github_workflows() # update the github workflows to your version of sandpaper
update_cache() # update the package cache to use the latest versions of the packages in your lesson

If you have a lesson outside of The Carpentries and do not want to do this manually, you can still get access to pull requests like this, and the workflow will remind you to do this with the following instructions:

Steps to Generate a New Token

1. :key: Go to https://github.com/settings/tokens/new to generate a new token with the repo and workflow scopes from your GitHub Account and give it a name that’s meaningful
2. :clipboard: Copy your new token to your clipboard
3. Go To https://github.com/YOUR-ACCOUNT/YOUR-REPOSITORY/settings/secrets/actions/new
   • enter SANDPAPER_WORKFLOW for the ‘Name’
   • :inbox_tray: paste your token for the ‘Value’

After that, your lesson will have the benefits of automated pull requests that keep you up-to-date!