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The Page Is Not The Lesson

The finger pointing at the moon is not the moon.

— variously attributed

I tweeted yesterday about using static website generator templates for lessons:

  1. Programmers follow many conventions to make code repos more usable, from having README, LICENSE, and CONDUCT files in the root directory to naming conventions, package structure, and having make test or npm run test do something useful.

  2. Every time I see an aggregation like this, I wish we had similar interoperability/discoverability conventions for tutorials. That doesn’t mean “one template to rule them all” any more than it means every software project must have exactly the same structure, but…

  3. …imagine a world in which every tutorial had a GLOSSARY file beside its README and LICENSE files so that you could easily find out what terms that lesson defined (which in turn would tell you what it was about)? Or a convention for structuring exercises…

  4. …similar to the conventions that programming languages have for structuring tests (where they are, what they’re called, etc.). There are standards for creating and packaging learning objects for use with learning management systems, but…

  5. …they are much too burdensome for most free-range teaching—it’s as if our only options were chaos or Enterprise Java. I hope some day that creating a lesson on GitHub is as easy (i.e., as well supported both technically and socially) as creating a Node project.

  6. One way forward could start with a change of perspective: instead of thinking a package as “code with some docs”, think about it as “docs with some supporting code”. What would we have to add to turn a site like https://readthedocs.org into a lesson hub?

  7. Auto-grading is a distraction in this context—it’s certainly not a must-have, not even for coding lessons. (Proof: textbooks have been around and useful for centuries without auto-grading.) But think about things like…

  8. …consistent numbering of exercises and figures across multiple source documents. Think about learning objectives that can be put in each individual lesson, but extracted and collated as a summary. All of these things…

  9. …can be done with existing tools, but they’re all harder and more fragile than documenting the parameters to a method or cross-referencing classes and their ancestors/decendants. (If your “solution” requires people to indent their YAML, it’s not a solution.)

  10. And yes, the analogy with reusing code is flawed—the Reusability Paradox is very real—but I believe discoverability and interoperability are worthwhile, achievable goals.

  11. How can I tell at a glance that a site or repo is a lesson rather than [noun]? What about the (human) language it’s in? Ditto its major topics. We’re done this part when I can search for “lesson in Spanish about JavaScript callbacks” with high signal-to-noise.

  12. This is part of why we wrote https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008469 (see also https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854): we should listen to librarians & teachers before we create more templates (but then, I think the world would be a better place if we all listened to librarians and teachers more…)

Much of the discussion that followed on Twitter and by email took the form, “If we build a good enough template, people will adopt it.” With respect, I think that if better templates were the solution, they would have worked by now. I have written several myself, including the first version of the Carpentries template; I’ve used several others, and a search on GitHub turns up dozens of others.

The problem is that templates help present the lesson but don’t help write it. For example, all of the templates I’ve looked at allow authors to write whatever they want for learning objectives. They don’t help connect those objectives together or check that the objectives are still consistent with the lesson’s content: “still” because lessons evolve over time, and people forget to check and update objectives just as they forget to check and update documentation and installation instructions for code. Just as UML doesn’t help developers solve the hard parts of their problems, static website frameworks don’t help teachers any more than a Microsoft Word or Google Doc template.

That’s a slight exaggeration: templates do help keep common values like the author’s email address consistent. However, the cost is very high: installing Jekyll or Hugo, writing YAML to configure them, and getting the right plugins in place (never mind keeping them up to date) is a hell of a cover charge. The payoff seems small, particularly if you aren’t already steeped in the technology, so on any given Thursday, most teachers really are better off using Word or Docs.

The Glosario project (site, repo) is an experiment to see if we can do better. Suppose you’re writing a lesson about data science using Markdown. Instead of using bold or [an arbitrary link](http://somewhere/#term) to highlight a definition, you either:

  1. refer to [the online glossary](https://glosario.carpentries.org/en/#term) (in your preferred language), or

  2. call an inline function like gloss('key', 'inline text') to generate that text and link (if you’re using something like R Markdown).

In both cases, tools can now tell which terms a particular lesson defines. Those terms can then be put in the <head> of a web page, stuffed in a database, or added to a summary page for the course as a whole. Doing this accomplishes two things:

  1. It makes the lessons more discoverable.

  2. It allows to build another tool for stitching lessons together. People will not manually highlight all of the terms they use in a lesson that they don’t define: it’s too much work, and requires too much re-work as the glossary evolves. However, it would be relatively straightforward to compare the text of a lesson against a glossary to determine what terms it depends on so that we can say, “You probably want to look at lessons X and Y before tackling lesson Z.”

No templating engine I know of will do this right now. Most of them won’t even do simpler but equally necessary things like create two-part IDs for the figures within chapters and then fill in references with chapter.figure.

Yes, I’ve used GitBook, Bookdown, and JupyterBook. No, they are not solutions for the 99.9% of our species that can’t or won’t spend their afternoons messing with Pandoc templates, LaTeX packages, and conflicts between multiple YAML configuration files.

So here’s what I’d like, and yes, I do think this would be a great project for someone doing a PhD in HCI: finish the tooling for Glosario, fold it into lessons written with the template of your choice, and tell us what you’ve learned about how to build it and about whether authors, instructors, and learners actually find it useful. It may seem like a small thing, but I bet it’s harder than it looks, and I bet we’ll learn a lot more from doing it than we expect. Most importantly, I think it would a good first step toward shifting our attention from the page to the lesson.

Punchcards Considered Harmful


Most people programming today have never punched a card, but all programming editors still treat code as lines of text—in other words, as if it still might have to fit onto punchcards. As I’ve been saying ranting for a while now, this is holding us back in ways we can barely recognize.

One example is YAML, or rather, the insistence that people must write complex nested data structures as indented lines of text. The rules are well-defined and simple cases are simple, but as anyone who has spent an hour wrestling with a Jekyll or Bookdown configuration file can attest, any complex case is an unproductive nightmare waiting to escape its cage.

So here’s a thought experiment. Imagine that every editor from Notepad to Vim to VS Code automatically displayed CSV files as editable tables. Instead of editing this:

book_filename: "r4de"
    fig: "Figure "
    tab: "Table "
    chapter_name: "Chapter "
output_dir: "docs"
delete_merged_file: false
new_session: true
  - index.Rmd
  - basics.Rmd
  - tidyverse.Rmd
  - rmarkdown.Rmd
  - package.Rmd
  - references.Rmd

people would read and edit something like this:

book_filename "r4de"
fig "Figure "
tab "Table "
chapter_name "Chapter "
output_dir "docs"
delete_merged_file false
new_session true

The file might actually be stored like this:

,,fig,"Figure "
,,tab,"Table "
,,chapter_name,"Chapter "

but if programmers could trust everyone’s favorite editor to render rows and columns as rows and columns, I believe that:

  1. most people would choose to use it instead of JSON, YAML, TOML, and STUMBL (OK, I made that last one up, but you weren’t sure, were you?) because

  2. they would find it easier to read and write nested structures if their editor gave them even this little bit of help and guidance.

But I don’t have any evidence for my second claim, which is where you (the ambitious grad student looking for a project) come in. Is there a difference in frustration quotient between YAML-in-a-text-editor and the same data in a table editor? Do people like the experience better if the table editor lives inside their usual editor? And can people find bugs faster or more reliably if nested structures are presented as tables rather than as indented text? My bet is “yes” for all three, but I don’t want you to trust me because I don’t want you to trust people—I want you to trust data.

And of course once this is working, the next experiment would be to add a tree editing widget to several common programming editors and see if it’s better, worse, or the same. I use [ a | b ] is my way of showing two editable cells side by side, and for fairness’ sake I think it’s essential to add these widgets to existing editors: many programmers will change operating system, citizenship, and gender before abandoning Emacs.

├──[ book_filename | "r4de" ]
│   ├──label
│   │  ├──[ fig | "Figure " ]
│   │  └──[ tab | "Table " ]
│   └──ui
│      └──[ chapter_name | "Chapter " ]
├──[ output_dir | "docs" ]
├──[ delete_merged_file | false ]
├──[ new_session | true ]

I don’t think “the other 99%” of humanity will use static site generators to write lessons unless we make them much (much) more approachable. Making configuration easier is just one part of that, but:

  1. it’s a part that can be used in many other places, and

  2. it’s a step toward finally ending the long, tyrannical reign of the punchcard.

Alpha Version of Software Tools in JavaScript

I have to fix two bugs in the examples, draw 91 diagrams, fill in an appendix on cognitive load, and then revise all 52,000 words, but the first draft is done. Feedback would be greatly appreciated: you can mail me or file issues in the book’s GitHub repository.

Title Pages Topic
Introduction 6
Systems Programming 20 Using callbacks to manipulate files and directories
Asynchronous Programming 22 Using promises to manage delayed computation
Unit Testing 12 Testing software piece by piece
File Backup 22 Archiving files with directory structure
Data Tables 16 Loading, saving, and manipulating tables efficiently
Pattern Matching 20 Using patterns to find things in data
Parsing Expressions 14 Turning text into code
Page Templates 18 Generating HTML pages from templates
Build Manager 22 Updating files that depend on other files
Layout Engine 24 Figuring out what goes where in a web page
File Interpolator 16 Managing source files that have been broken into pieces
Module Loader 16 Loading source files as modules
Style Checker 16 Checking that code conforms to style guidelines
Code Generator 14 Modifying code to track coverage and execution times
Documentation Generator 16 Generating documentation from comments embedded in code
Module Bundler 18 Turning many files into one
Package Manager 12 Getting and installing packages
Virtual Machine 16 Assembling and running low-level code
Debugger 18 Running programs under the control of a breakpointing debugger
Conclusion 2 Where we have been and where you could go next
Bibliography 2
License 4
Code of Conduct 2
Contributing 6
Cognition 2
Glossary 20
Links 6
Authors 6
Total 398

Pickled Carrots

By popular request, here is my spouse’s recipe for pickled carrots, which is derived from the one in Topp and Howard’s excellent The Complete Book of Small-Batch Preserving. Note that this is a canning recipe, not a cold pickle. Note also that the original recipe calls for only ¼ tsp of hot pepper flakes per jar, to which we say, “Bah.”

pickled carrots
Medieval ingredient metric
3 tbsp finely chopped fresh oregano or 1 tbsp (15 mL) dried 45 mL
1-3 tsp hot pepper flakes (per jar) 5-15 mL
2 small cloves garlic 2
1 lb peeled baby carrots 500 g
1 ½ cups white vinegar 375 mL
½ cup granulated sugar 125 mL
⅓ cup water 75 mL
1 tsp pickling salt 1 mL
  1. Remove the hot jars from the canner and add one garlic clove and your desired volume of chili flakes to each jar.

  2. Pack in the carrots (see picture) leaving 1cm (½ inch) of head space.

  3. Combine vinegar, sugar, water, and salt in a small saucepan and bring to a boil.

  4. Pour hot liquid over carrots (in jars) to within ½ inch of the top.

  5. Process for canning: 15 minutes for 500 mL jars.

A 2lb (approx. 1kg) bag of baby carrots will make 1750 mL of pickle. We usually use 250 mL wide-mouth jars—they make great gifts.

Steps in Order

Our book Research Software Engineering with Python has finally gone to the publisher. We will undoubtedly still have to make revisions, but the ideas and examples are complete. Our intended readers are captured in these three learner personas:

  • Amira Khan completed a master’s in library science five years ago and has since worked for a small aid organization. She did some statistics during her degree, and has learned some R and Python by doing data science courses online, but has no formal training in programming. Amira would like to tidy up the scripts, data sets, and reports she has created in order to share them with her colleagues. These lessons will show her how to do this.

  • Jun Hsu completed an Insight Data Science fellowship last year after doing a PhD in Geology and now works for a company that does forensic audits. He uses a variety of machine learning and visualization packages, and would now like to turn some of his own work into an open source project. This book will show him how such a project should be organized and how to encourage people to contribute to it.

  • Sami Virtanen became a competent programmer during a bachelor’s degree in applied math and was then hired by the university’s research computing center. The kinds of applications they are being asked to support have shifted from fluid dynamics to data analysis; this guide will teach them how to build and run data pipelines so that they can pass those skills on to their users.

We organized the book around a running example: the verification of Zipf’s Law using a set of classic English novels in an open, reproducible, and sustainable way. (People often conflate these three ideas, but they are distinct). To do that, we teach readers to do these things:

  1. Use the Unix shell to efficiently manage data and code.
  2. Organize small and medium-sized data science projects.
  3. Write Python programs that can be used on the command line.
  4. Use Git and GitHub to track and share work.
  5. Work productively in a small team where everyone is welcome.
  6. Use Make to automate complex workflows.
  7. Enable users to configure software without modifying it directly.
  8. Test software and know which parts have not yet been tested.
  9. Find, handle, and fix errors in code.
  10. Publish code and research in open and reproducible ways.
  11. Create Python packages that can be installed in standard ways.

The order is important because later skills depend on earlier ones, but also because we want people to be able to stop part way through and still have a workable research process. If you only get through the fourth chapter, for example, you’ll be able to back up your work, share it with others, and re-run analyses with a single command. Another chapter and you’ll be ready to collaborate in a team; one more after that, and you’ll be able to capture your workflows in re-runnable ways.

We don’t believe any one book can serve everyone’s needs, but we hope this one will help people who already know how to write a bit of code figure out what to learn next and what “done” looks like. The HTML version of the book will stay online for free and forever; we’ll advertise the printed and e-book versions as soon as they become available. If you find it useful, please let us know (and please also let us know about any errors or murky wording you stumble over).

This book has been over twenty years in the making; many thanks to my co-authors Damien Irving, Kate Hertweck, Luke Johnston, Joel Ostblom, and Charlotte Wickham for finally making it a reality. All royalties from the book will be donated to The Carpentries, an organization that teaches foundational coding and data science skills to researchers worldwide.