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What’s wrong with computational notebooks?

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Re: What’s wrong with computational notebooks?

#71

Post by ssivark »

snapetom wrote: post #42
azhenley wrote: post #10

Co-author of the study here. Let me know if you have any questions or how you overcome some of the problems we identified!

I just wanted to say thank you. Many of the points in your study strikes a nerve. Part of my responsibility at my last job was to introduce good software engineering practices. What happens? The data scientists go rogue and start running notebooks left and right. How do they productionize their work? Well, they don't. They were academics. All they know is that the models ran fine in their notebooks on their laptops.…

I just happened to be reading Peter Naur's "Programming as theory building" recently. It strikes me that taking its theme even a little seriously helps understand why notebooks are so popular. Notebooks happen to be convenient tools for exploring a new domain (interactively). Irrespective of how much software purists might complain, conventional software engineering provides very few tools/solutions/practices for that process. The wretched state of interactive debugging (in most languages) is a simple example.

As someone who spends a substantial amount of time working with both modes (writing research code in Jupyter notebooks, and writing production code as python modules), notebooks scratch certain itches that IDEs typically don't even come close to. (Some recent progress on add-ons in Javascript-based editors is potentially interesting, because that might help marry the strengths of the two)

In my experience, in the evolution of code from Jupyter notebooks to repositories of production code as part of any project, there comes a "right time" to switch from the former to the latter. And this can typically only be learned with experience.

Re: What’s wrong with computational notebooks?

#72

Post by goatlover »

rabryan35 wrote: post #7

No mention of https://observablehq.com notebooks? They’re the best I’ve found in the “Share and collaborate” and “As products” category. JupyterLab is still pretty great for exploratory stuff, but visualization possibilities in observable are incredible.

Problem is that Javascript doesn't have the scientific computing ecosystem that Python, R and Julia have. Jupyter supports those languages and any others that people write kernels for. And you can also execute bash, JS, CSS and HTML directly in python notebooks with magic commands.

Re: What’s wrong with computational notebooks?

#73

Post by azhenley »

thanatropism wrote: post #68
azhenley wrote: post #10

Co-author of the study here. Let me know if you have any questions or how you overcome some of the problems we identified!

Is there opportunity for cross-pollination of your research with the spreadsheet literature?

Yes! Not only that, but with all of the end-user programming research. I did some studies on LabVIEW programmers before and I noticed a lot of the same phenomenon with data scientists. They have a lot of domain knowledge, some programming experience, but usually do not use software engineering best practices or tools (e.g., unit testing, code reviews, automated refactoring). All of this is very understandable but reveals a lot of potential for tools to better support them.

See Yestercode [1] and CodeDeviant [2], two tools that I specifically designed for LabVIEW programmers to refactor and test their code without expecting them to behave like traditional software engineers.

[1] http://web.eecs.utk.edu/~azh/pubs/Henley2016VLHCC_Yestercode...

[2] http://web.eecs.utk.edu/~azh/pubs/Henley2018VLHCC_CodeDevian...

Re: What’s wrong with computational notebooks?

#74

Post by closed »

azhenley wrote: post #10

Co-author of the study here. Let me know if you have any questions or how you overcome some of the problems we identified!

Interesting study! I'm curious what shadowing 15 R data scientists would look like, since it seems to resolve some of the pain points around caching results, debugging, and scaling.

This is a very minor question (and I am not concerned about risk to participants)--when you say they signed consent "in accordance with our institutional ethics board", are you talking about Microsoft, one of the two universities, or all?

Re: What’s wrong with computational notebooks?

#75

Post by chirau »

jpeloquin wrote: post #66
chirau wrote: post #43

Earlier quoted context omitted.

Be careful what you wish for. Hot reloads can become very expensive. Especially when it comes to computationally heavy tasks that notebooks are built for. If you decide you want hot reloads by default, it'd mean each time you click on a cell and then click on another you'd be restarting the whole notebook. If you had massive datasets you were loading or other args that you were parsing manually or at prompt, you'd ha…

> I think it is a good thing that notebooks separate instructions and re-execute manually by default. The cost of the alternative is just too high. Maybe add a "lock" toggle so a user can block a cell from being automatically executed? The heavy numeric setup tasks could then be gathered in a few cells and locked, leaving the lighter plotting & summary stats cells free to update reactively.

Toggle???

Toggle a whole environment and intrepeter's behavior? Do you know how much architecture that would involve? That's like trying to tell IDLE to be able to both delete or keep your variables on exit, or the JVM to have a toggle switch for memory and garbage management.

Why doesn't the developer make themselves useful and simply write a save function that freezes their buffer variable values to a text, json or SQLite file that they can read from or stream rather than trying to set back a whole community years of progress in an effort to accommodate perhaps entitled or lazy devs.

Can you even imagine the architectural costs of trying to accommodate streaming data and timestamped data as opposed to you just writing your own stuff to file?

Re: What’s wrong with computational notebooks?

#77

Post by okennedy »

moultano wrote: post #5

I want a notebook where causality can only flow forward through the cells. I hate notebook time-loops where a variable from a deleted cell can still be in scope. 1. Checkpoint the interpreter state after every cell execution. 2. If I edit a cell, roll back to the previous checkpoint and let execution follow from there. I can't tell you how many times I've seen accidental persistence of dead state waste hours of peopl…

Check out our reproducibility focused notebook Vizier (https://vizierdb.info). In Vizier, inter-cell communication happens through spark dataframes (and we're working on other datatypes too. This makes it possible for Vizier to track inter-cell dependencies and automatically reschedules execution of dependent cells. (It also makes Vizier a polyglot notebook :) )

Re: What’s wrong with computational notebooks?

#78

Post by ngcc_hk »

What is wrong with life? Many but let us appreciate how to use it more instead of seemingly criticise it.

The world is so much better with you alive. So is the founded tool of computational notebook. Not sure I read it covered R notebook which is really good to share info and analyst. Just wonder how to use it better.

Of course they can always improve on it. But I would promote more expansion - How about a lisp notebook, a clojure notebook, a js notebook and a forth notebook.

The real problem is can you have oo notebook ... it is more “serial” and graphic and data. But not for the “messy” class or trigger Based system. Hence if I may, the real problem is the scoping. It is so hard to visualise a live oo system. Unlike a live functional or even a stack based system.

It is not life that is the problem. Even useless life has its use, as long as it is alive. But if it is not reaching there an alternative may have to think about. Just like we cannot be there we send in our voyagers outside solar system.

Be long and prosper.

Re: What’s wrong with computational notebooks?

#80

Post by anonsivalley652 »

There are these and other problems with CNs:

0. They try to be "be-all, end-all" proprietary container documents, so they lack generality, compatibility and embeddability. It would be better if live code try-out snippets were self-contained and embeddable in other documents: HTML, other software, maybe PDF, LaTex or literate programming formats. Maybe there should be standard, versioned interpreters for each kind of programming language in WebAssembly and cached for offline usage by the browser for inclusion in documentation, papers, etc.?

1. For prototyping, it is better to have try-out live code (and/or REPLs with undo) for prototyping like what is Xcode/iOS Playgrounds for Swift or ReInteract was for Python.

2. Computational notebook software, that I've seen, are terrible, complex, fragile and messy to install. The ones I've seen make TeXLive look effortless by comparison.

3. Beyond replicability what goal(s) are CN really trying to solve?

3.0. For replicability itself, why not have a GitLab/BitBucket/GitHub repo for code and a Docker/Vagrant container one-liner that grabs the latest source when built? Without a clear, consistent and simple build process, there is no replicability, only wasted time, headaches and fragile/messy results.

3.1. Are CNs "hammers" for "nails" that don't exist?

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