Transitioning Carpentries Lessons

This repository contains a workflow for transitioning Carpentries lessons built from the all-in-one infrastructure (aka "The Lesson Template") to the decoupled/centralised infrastructure (aka "The Carpentries Workbench"). The intent of this was explicitly to provide a workflow that could transition all of the 61 official Carpentries lessons. It is not guaranteed to work for any lessons outside of The Carpentries.

If you want to use this workflow here are the steps:

1. install R, Python, and the gh utility (see the usage section)
2. add a lesson R script using bash add-lesson.sh <ORG>/<LESSON>
3. run make sandpaper/<ORG>/<LESSON>.json to test and iterate on the transformation (see the overview section for details)

This workflow will create a submodule for this that will be kept up-to-date until you release the transitioned lesson.

The release process uses tools built for R, python, Git, and BASH and is described in The Transition Workflow Documentation and The Release Workflow Documentation. Tests of the release workflow are outlined in The Release Workflow Testing Documentation

Warning This process is necessarily destructive and can only be perforemd one-way from carpentries/styles to The Carpentries Workbench. Once a lesson is transitioned, it can not transition back.

How To Clone

This repository uses submodules which do not automatically get propogated when you clone. The submodules are kept up-to-date via a GitHub action and the fetch-submodule.sh script.

To transform one lesson

If you wish to transform one lesson, you can clone this without pulling down the submodules. This will save space and bandwidth and is generally the right choice. There are two git commands you need to bootstrap the lesson.

git clone https://github.com/carpentries/lesson-transition.git
cd lesson-transition
git submodule update --init git-filter-repo # make sure `git-filter-repo` is available

To transform all lessons

If you have a good strong internet connection and you need to transform a lot of repositories at once, then you may need to fetch all the submodules. You can do so with the --recurse-submodules option.

git clone --recurse-submodules https://github.com/carpentries/lesson-transition.git

git pull --recurse-submodules

Updating when submodules update

There will be times when the submodules update on GitHub and you forget to use --recurse-submodules. When this happens, you will end up with mysterious staged changes in your local clone. You can run make -B modules and the submodules will recurse for you (note that this has the same effect as --recurse-submodules and you may see an increase in the size of your repository).

Removing submodules

There are two ways to remove submodules from this repository:

1. transform a lesson to The Workbench. This will create a file called relase/ORG/REPO-invalid.hash.
2. add the repository in the form of ORG/REPO to .module-ignore

Either one of these will signal to fetch-submodule.sh that the submodule is no longer used and it should be removed from this repository.

If you do this by accident, you can use this pattern to restore the module:

git restore --staged .gitmodules ORG/REPO
git restore .gitmodules ORG/REPO

Submodules removed on lesson release

When a lesson is transitioned to use The Workbench, it will be automatically deleted from this repositoriy via GitHub Actions. When you pull from the remote repository, the module will be gone, but the folder will remain. These folders cannot be cleaned with git clean -fd, so you will need to manually remove them The easiest way to do this is to use the git log and xargs, but NOTE: this will destroy any uncommitted or unstaged work:

git status --porcelain | awk '{print $2}' | xargs rm -r

Storage requirements

Warning

Cloning this repository with all the submodules will take a lot of bandwidth and space. As of this writing (commit 030f9cf), the weight of the repository is ~3 GB

During the transition, each of the lessons gains an entirely new set of commits, which could double the size of the lesson repository (though, it will almost always be less than that), but in terms of the lesson-transition/ directory on your machine: the size will triple if you clone this repository AND transform all of the lessons. Below are tables that demonstrate the sizes estimated of each of the lesson programs:

table: Official Lessons (breakdown in official-repo-sizes.csv)

GitHub Organisation	Repo Size	Required (3x Repo Size)
carpentries	63.55MB	190.65MB
datacarpentry	1.42GB	4.27GB
librarycarpentry	284.96MB	854.88MB
swcarpentry	334.73MB	1004.2MB
TOTAL	2.09GB	6.28GB

table: Community Lessons (breakdown in community-repo-sizes.csv)

GitHub Organisation	Repo Size	Required (3x Repo Size)
carpentries-incubator	5.04GB	15.12GB
carpentries-lab	199.08MB	597.24MB
TOTAL	5.24GB	15.71GB

Overview

In general, there are two commands you would want to use:

Purpose	command	effect
Test a lesson transition	make sandpaper/<org>/<repo>	creates a test transition of a lesson by making a copy of the submodule, and transforming it inside of the sandpaper/ directory. This transformation adds some additional filters to the commit messages so that any issue or pull request references are masked. This prevents authors from getting notifications if you push it up to a testing repository.
Release a lesson transition (irreversible)	make release/<org>/<repo>	transitions a lesson and reconfigure the source repository to use The Workbench. **This is irreversible, so be sure that this is what you want to do **

The test transition workflow is generally modelled like this:

---
title: "Workbench Transition Workflow"
---
flowchart TD
    classDef styles fill:#001483,color:#FFF7F1,stroke-width:1px
    classDef workbench fill:#FFC700,stroke:#333,stroke-width:1px

    subgraph github.com/ORG
    GH[("fab:fa-github LESSON")]
    end

    
    FINAL{{"TRANSFORMATION SCRIPTS"}}    
    subgraph  ORG/
    SLS{{LESSON.R}}
    SL[/"fab:fa-git-alt LESSON/"\]:::styles
    end

    subgraph sandpaper/ORG/
    WL(["fab:fa-git-alt LESSON/"]):::workbench
    end

    GH -.->|"2. git pull"| SL
    SLS -.-> |"1. submodule"| SL

    SL --> FINAL
    FINAL --> |"3. transform"| WL

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When pushing to GitHub, the flow looks like this:

---
title: "Workbench Transition Workflow (simplified)"
---
flowchart TD
    classDef styles fill:#001483,color:#FFF7F1,stroke-width:1px
    classDef workbench fill:#FFC700,stroke:#333,stroke-width:1px

    subgraph github.com/ORG
    GH[("fab:fa-github LESSON")]
    end

    
    FINAL{{"TRANSFORMATION SCRIPTS"}}    
    subgraph  ORG/
    SLS{{LESSON.R}}
    SL[/"fab:fa-git-alt LESSON/"\]:::styles
    end

    subgraph sandpaper/ORG/
    WL(["fab:fa-git-alt LESSON/"]):::workbench
    end

    GH -.->|"2. git pull"| SL
    SLS -.-> |"1. submodule"| SL

    SL --> FINAL
    FINAL --> |"3. transform"| WL
    FINAL ==>|"4. move branches"| GH
    WL ==>|"5. push --force fa:fa-shuffle"| GH

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Expanded versions of these graphs can be found in the Process section of this README.

For details about the differences between styles and the workbench, you can look at the transition guide.

Motivation

There are over 100 lessons in The Carpentries, Carpentries Lab, and Carpentries Incubator combined and they are all built in a slightly different way.

In addition to the difference between kramdown (Jekyll) syntax and Pandoc (Workbench/R Markdown) syntax, the styles lessons contain a lot of commit history that is unrelated to the lesson content itself. Some R-based lessons contain commits of generated output like images that bloat the repository.

Transitioning the content to use Pandoc syntax and the Workbench folder structure is a good enough approach, but we are still left with the previous commits that are not related to the lesson itself. These extra commits are a burden on the repository as they take up extra megabytes of space in the git database.

Thus, we are going one step further and removing all commits that are not strictly lesson content. By removing these commits, we distill the commit history to those that are relevant so that it paints a clearer picture of the lesson development timeline and reduces the cognitive load needed to understand how the lesson was created.

Note: Excluding irrelevant commits from the history has precedent within The Carpentries! Prior to 2015, Software Carpentry lessons all lived in a monorepo called bc. In 2015, there was a need to update the infrastructure, but it did not make sense to include the entire history of the shell lesson in the git lesson (and vice versa), so the new repositories were seeded from the initial commits for each relevant lesson. Take for example, the initial commit with pages in swcarpentry/git-novice and the initial commit with pages for git-novice in the bc repo. Both of these commits were made on the same time, but one has a parent commit and the other one doesn't.

Background

Since 2016, Carpentries lessons were based on a custom template that used the Jekyll static site generator because this was by far the easiest and most reliable way to host a website using GitHub. Lessons built from the template also contained styling components in HTML, CSS, and JavaScript; validation scripts in Python, and workflow tooling in BASH, Make, and R. Because these components lived inside the lesson itself, the only way to update them was to make a pull request from the source repository, which would add commit history that was unrelated to the lesson itself. This brought in a number of issues:

1. Lessons were often out of date in terms of styling and tooling because the process of merging in a separate repository is off-label use of git
2. (idiomatic) The default branch had to be gh-pages to allow GitHub to deploy the content to a website
3. Lesson publications became arduous because authors to styles needed to be filtered out from the history in order to compile the author list for the lesson
4. Jekyll was not built in a way that could be easily distributed across multiple platforms to people who were not software developers
5. Lessons based in R Markdown contained committed artefacts, which vastly increased the size of the repository.

The workbench separates the tools and styling from the content, so a lesson can be created and authored without the contributors worrying about keeping the lesson or tools up-to-date.

Process

The process works in the following steps:

1. (manual step) create file named <program>/<lesson>.R (e.g. swcarpentry/r-novice-gapminder.R)
2. provision template with Rscript establish-template.R template/
3. add/fetch git submodule of the repository for reference with fetch-submodule.sh <program>/<lesson>
4. run filter-and-transform.sh sandpaper/<program>/<lesson>.json <program>/<lesson>.R, which does the following
   i. performs a fresh clone of the submodule into sandpaper/program/lesson/
   ii. use git-filter-repo to exclude commits associated with carpentries/styles
   iii. apply transformations in transform-lesson.R to modify kramdown syntax to pandoc syntax and move folders
   iv. apply additional needed transformations in program/lesson.R to fix any components that were not covered in the previous step
   v. creates commits and records them in sandpaper/program/lesson.json

Note: Not all of the repositories represented here are official Carpentries Lessons. Only swcarpentry, datacarpentry, librarycarpentry, and carpentries lessons are official

These scripts require a setup with R and access to the internet. It is currently a work in progress and may evolve in the future.

This process is fully demonstrated in the workbench testing workflow:

flowchart TD
    classDef styles fill:#001483,color:#FFF7F1,stroke-width:1px
    classDef workbench fill:#FFC700,stroke:#333,stroke-width:1px
    classDef r fill:#205959,color:#FFF7F1
    classDef script fill:#D2BDF2
    
    subgraph github.com/ORG
    GH[("fab:fa-github LESSON")]
    end
    
    subgraph interactive
    YOU{"USER fa:fa-user"}
    MK{{"make release/ORG/LESSON.json"}}
    end
    
    FS{{"fetch-submodule.sh"}}:::script
    FT{{"filter-and-transform.sh"}}:::script
    GFR(["git-filter-repo/ fa:fa-database"]):::script
    TL{{"transform-lesson.R"}}:::r
    FR{{"functions.R"}}:::r

    
    subgraph  ORG/
    SLS{{LESSON.R}}:::r
    SL[/"fab:fa-git-alt LESSON/"\]:::styles
    end

    subgraph release/ORG/
    WL(["fab:fa-git-alt LESSON/"]):::workbench
    LOG["(output log) LESSON-filter.log"]
    COMMITS["(commits) LESSON.json"]

    end

    YOU ==> MK
    GH -.-> SL
    MK --> FS
    SLS -.-> FS
    MK --> FT
    FS -->|"0. provision submodule"| SL
    SL --> FT 
    FT -->|"1. makes a copy fa:fa-code-fork"| GFR
    GFR -->|"2. filter styles commits fa:fa-filter"| TL 
    FR ---|"common transformations"| TL
    TL -->|"3. transformation + commit"| SLS
    SLS -->|"4. final cleanup + commit"| TL
    TL --> WL
    TL -.-> LOG
    TL -.-> COMMITS

Loading

During the release process, the final transition workflow adds a step where the lesson repository is transformed using the GitHub API:

---
title: "Workbench Transition Workflow"
---
flowchart TD
    classDef styles fill:#001483,color:#FFF7F1,stroke-width:1px
    classDef workbench fill:#FFC700,stroke:#333,stroke-width:1px
    classDef r fill:#205959,color:#FFF7F1
    classDef script fill:#D2BDF2

    subgraph github.com/ORG
    GH[("fab:fa-github LESSON")]
    end
    
    subgraph interactive
    YOU{"USER fa:fa-user"}
    MK{{"make release/ORG/LESSON.json"}}
    end
    
    FINAL{{"final-transition.R"}}:::r
    FS{{"fetch-submodule.sh"}}:::script
    FT{{"filter-and-transform.sh"}}:::script
    GFR(["git-filter-repo/ fa:fa-database"]):::script
    TL{{"transform-lesson.R"}}:::r
    FR{{"functions.R"}}:::r

    
    subgraph  ORG/
    SLS{{LESSON.R}}:::r
    SL[/"fab:fa-git-alt LESSON/"\]:::styles
    end

    subgraph release/ORG/
    WL(["fab:fa-git-alt LESSON/"]):::workbench
    LOG["(output log) LESSON-filter.log"]
    COMMITS["(commits) LESSON.json"]
    HASH["(updated hashes) LESSON{,-invalid,-commit-map,-ref-map,suboptimal-issues}.hash"]

    end

    YOU ==> MK
    MK -->|"0. provision submodule"| FS 
    GH -.->|"pull"| SL
    SLS --> FS
    MK --> FINAL
    FR -.- FINAL
    FS --> SL
    SL --> FINAL
    FINAL --> FT
    FT -->|"1. makes a copy fa:fa-code-fork"| GFR
    GFR -->|"2. filter styles commits fa:fa-filter"| TL 
    FR -.-|"transform() fab:fa-r-project"| TL
    TL -->|"3. transformation + commit"| SLS
    SLS -->|"4. final cleanup + commit"| TL
    TL --> WL
    TL -.-> LOG
    TL -.-> COMMITS
    FINAL -.-> HASH
    GH <===> |"push --force fa:fa-shuffle"| WL
    FINAL ===> |"setup_github() fab:fa-r-project"| GH
    

Loading

The repositories that have previously been transferred can be found in repos.md.

Beta Phase

The Workbench beta phase steps are described in full at The Workbench website. The process of moving lessons in each part of the beta phase are documented in The Beta Phase Workflow document.

In short, the first part of the beta phase involves converting a snapshot of a lesson to use The Workbench and host it on a separate GitHub organisation.

The second part of the beta phase involves converting the lesson to use The Workbench in place and moving a snapshot of the old version to a branch called "legacy"

Maintainers should take care to make sure they do not accidentally merge hundreds or thousands of commits during the conversion.

Keeping your clone up-to-date

Once a lesson has transitioned to use The Workbench, the default branch of the lesson will be altered. Here are the steps you should perform to make sure you do not end up with a borked repository:

Easy mode: delete/rename your local copy and re-clone

This method is guaranteed to prevent merge conflicts and give you a clean slate.

Advanced: branch name shuffle

If you want to keep your local copy, here is how you can modify your lesson to update without merge conflicts:

For Markdown Lessons

Markdown lessons will have the default branch set to be gh-pages. In the Workbench, this branch serves rendered HTML, so we will need to change the name of this branch to legacy/gh-pages using a similar process that GitHub recommends after a default branch name change:

git checkout gh-pages              # make sure you are gh-pages
git branch -m gh-pages legacy/gh-pages               # rename the gh-pages branch to legacy
git fetch origin                                     # fetch changes from GitHub
git branch -u origin/legacy/gh-pages legacy/gh-pages # make sure your legacy branch tracks
git checkout main                  # switch to the brand-new main branch
git remote set-head origin -a      # set main branch to be your local default

Here's what it looks like with output:

git checkout gh-pages              # make sure you are gh-pages
# Already on 'gh-pages'
# Your branch is up to date with 'origin/gh-pages'
# git branch -m gh-pages legacy/gh-pages      # rename the gh-pages branch to legacy
git fetch origin                              # fetch changes from GitHub
# remote: Enumerating objects: 415, done.
# remote: Counting objects: 100% (415/415), done.
# remote: Compressing objects: 100% (193/193), done.
# remote: Total 415 (delta 197), reused 415 (delta 197), pack-reused 0
# Receiving objects: 100% (415/415), 69.97 KiB | 1.19 MiB/s, done.
# Resolving deltas: 100% (197/197), done.
# From https://github.com/zkamvar/transition-test-2
#  + d5702e0...3fb3008 gh-pages        -> origin/gh-pages  (forced update)
#  * [new branch]      legacy/gh-pages -> origin/legacy/gh-pages
#  * [new branch]      main            -> origin/main
#  * [new branch]      md-outputs      -> origin/md-outputs
git branch -u origin/legacy/gh-pages legacy/gh-pages # make sure your legacy branch tracks
# branch 'legacy/gh-pages' set up to track 'origin/legacy/gh-pages'.
git checkout main                  # switch to the brand-new main branch
# branch 'main' set up to track 'origin/main'.
# Switched to a new branch 'main'
git remote set-head origin -a      # set main branch to be your local default
# origin/HEAD set to main

For R Markdown Lessons

R Markdown lessons will have the default branch set to be main. The rendered output of this branch lives in gh-pages. The new branches will histories that will have different commits, so the process for updating is similar to that of the Markdown lessons, with two extra steps to protect your main branch.

git checkout main                  # make sure you are on main
git branch -m main legacy/main     # change 'main' to legacy
git checkout gh-pages              # switch to gh-pages
git branch -m gh-pages legacy/gh-pages       # rename the gh-pages branch to legacy
git fetch origin                             # fetch changes from GitHub
git branch -u origin/legacy/main legacy/main # make sure your legacy branches track
git branch -u origin/legacy/gh-pages legacy/gh-pages 
git checkout main                  # switch to the brand-new main branch
git remote set-head origin -a      # set main branch to be your local default

Here's what it looks like with output (NOTE: ZHIAN KNOWS THIS OUTPUT IS OUTDATED, BUT THE GIST IS STILL THE SAME)

git checkout main                  # make sure you are on main
# Already on 'main'
# Your branch is up to date with 'origin/main'
git branch -m main old             # change 'main' to a local 'old' branch
git checkout gh-pages              # switch to gh-pages
# branch 'gh-pages' set up to track 'origin/gh-pages'.
# Switched to a new branch 'gh-pages'
git branch -m gh-pages legacy      # rename the gh-pages branch to legacy
git fetch origin                   # fetch changes from GitHub
# remote: Enumerating objects: 5004, done.
# remote: Counting objects: 100% (5004/5004), done.
# remote: Compressing objects: 100% (2010/2010), done.
# remote: Total 5004 (delta 2970), reused 5000 (delta 2966), pack-reused 0
# Receiving objects: 100% (5004/5004), 39.98 MiB | 32.57 MiB/s, done.
# Resolving deltas: 100% (2970/2970), done.
# From https://github.com/[PROGRAM]/[LESSON]
#  + 78697dd...087da6e gh-pages   -> origin/gh-pages  (forced update)
#  + 8e955fe...f6eaf66 main       -> origin/main  (forced update)
#  * [new branch]      legacy     -> origin/legacy
#  * [new branch]      md-outputs -> origin/md-outputs
git branch -u origin/legacy legacy # make sure your legacy branch tracks
# branch 'legacy' set up to track 'origin/legacy'
git checkout main                  # switch to the brand-new main branch
# branch 'main' set up to track 'origin/main'.
# branch 'main' set up to track 'origin/main'.
# Switched to a new branch 'main'
git remote set-head origin -a      # set main branch to be your local default
# origin/HEAD set to main

Usage

Requirements

This tool requires Git, R, Python, BASH, and Make to convert the lessons. There is one make command that uses the gh github command line interface. This will also provision pandoc for you if you do not have one on your computer.

The tool used to filter commits is a python tool called git-filter-repo and we have a copy as a submodule of this project.

The R packages required are provided in the renv.lock file.

Adding a new lesson

To add a lesson for translation, there are two steps:

1. Use bash add-lesson.sh [organization]/[repository] add an R script with the repository name under a folder with the organisation name (e.g. swcarpentry/r-novice-gapminder.R or datacarpentry/R-ecology-lesson.R).
2. run make modules to register it as a submodule (this step is also automatically run when the repository is pushed).

Bootstrapping infrastructure

Note

If you have never used {renv} before, then you will need to manually confirm that you want to use {renv} in an interactive R session. To do this, open R after you have cloned this repository and {renv} will bootstrap itself and then print a message on your screen informing you that it wants to create a global package cache and where it exists.

The infrastructure will bootstrap itself (so long as you have the Requirements installed) when you run a conversion command. This will include:

0. The lesson submodule
1. R package cache
2. The Workbench template
3. pandoc version 2.19.2 (the one used in RStudio by default)

To bootstrap the infrastructure without converting lessons, you can run the following targets:

make template modules

This will bootstrap the packages used for the scripts, create the sandpaper template, and update the git submodules

Updating R packages

To update the R packages used for translation, you can run make update

Individual targets

To make an individual target, run

make sandpaper/datacarpentry/R-ecology-lesson.json

Parallel processing

To run everything from scratch with 7 threads

rm -rf sandpaper/
make -j7

For the curious, this is the path of the makefile for a single target:

Sending lesson previews to GitHub

Note: this is for creating the lesson previews. For deploying a full transition, see the Release Workflow Document.

Because my changes will be stacked on top of the last commit of the previous lesson, every time a new commit is added or I change something in the build process, I will need to burn it all down and rebuild these lessons so that I do not end up with weird merge conflicts or a force-pushed history, thus I need to be able to do the following from the command line:

1. create repositories
2. assign the repositories to bot teams.
3. destroy repositories that are outdated in the past.

I have created a sandbox organisation where I know I can break things if I need to set up or tear down things. I have given the Carpentries Apprentice admin access so that I do not risk my own token being used to create and delete repositories.

To send lessons to GitHub, you need to make sure you have the correct tokens set up from GitHub in addition to your GitHub PAT, which will give you repo access:

• NEW_TOKEN to create and push the new repository
• BOT_TOKEN to assign the bots team to the repository
• DEL_TOKEN to delete a repository.

In testing, I set these tokens to expire the next day.

Because I do not want to keep these hanging around my BASH environment, and because I want to be difficult, I am using a vault secrets engine called tr by running vault server -dev in a separate window and then:

 # note the blank space before these commands hides these from the shell history
 vault secrets enable -version=2 -path=tr kv
 vault kv put -mount=tr auth \
bot=<token> \
del=<token> \
new=<token>

From there, I can use ./pat.sh bot to extract the bot token so that it can be used with the create-test-repo.sh script:

BOT_TOKEN=$(./pat.sh bot) NEW_TOKEN=$(./pat.sh new) \
create-test-repo.sh carpentries-incubator/citable-software bots fishtree-attempt

There is also the github target which will first delete any repositories you have created with this script and then re-create and upload them:

BOT_TOKEN=$(./pat.sh bot) DEL_TOKEN=$(./pat.sh del) \
make github

Notes

The transform-lesson.R script is meant to serve as a generalized method for converting lesson content from one engine to the other. It does the majority of the heavy lifting, but it can not completely convert lessons perfectly. Because each lesson is built in a slightly different way and kramdown (Jekyll's markdown parser) allows for patterns that would be invalid in any other parser, the conversion is not 100%. This additional R script allows you to make additional changes such as moving files or fixing errors. This file can be blank if there are no changes you wish to make

If your lesson is in a repository that does not belong to an official carpentries account, you will need to append the DIRS varaible in the makefile.

Requirements

This repository has package management via {renv}, so there are two steps to getting set up:

1. install R
2. Open R in this repository. {renv} should prompt you about using a central cache. Select yes.
3. Run make restore.

This will restore the renv session to the correct state so that you can convert the lessons contained with make

The packages used in this script are the same packages that are used in {sandpaper}, you can follow the setup instructions to get this script working .

Post translation

After a lesson is translated it lives in a brand new repository that will have three commits:

1. the bootstrap of the new lesson
2. the first pass of transform-lesson.R
3. Any other changes dictated by your custom script.

To get this to GitHub, I like to use the {usethis} package. For this operation, you will need to set up your GitHub PAT. I wrote up a tutorial to set up your PAT via R that may be helpful.

If, however, you are on Linux and find yourself in credentials hell, you might find solace in Danielle Navarro's blog post from August on setting up credentials for Ubuntu

Steps for uploading the lesson and activating github pages

Here, I'm using the fishtree-attempt, which is a pun on Carpentries (fish: carp, tree: ent, attempt: tries), but more importantly, it is a sandbox organisation in which I can comfrotably destroy and re-create lessons at will so that I can test out the translation features.

You should use your own account for this as you will likely not have access to the data-lessons organisation.

# In the directory of the new lesson
library(usethis)
use_github(organization = "my-organisation")

After a few minutes, the lesson will be sent to GitHub and build the site, but the pages need to be activated, which you can do via usethis:

# In the directory of the new lesson
library(usethis)
use_github_pages()