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What’s wrong with computational notebooks?

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Re: What’s wrong with computational notebooks?

#41

Post by xixixao »

This is a great list, and totally matches my experience. I also agree this is solvable with tooling.

A) VS Code / IDE needs to be the primary editor B) Results are not stored with source C) Export (build) allows packaging for whatever platform.

Python notebooks especially also use some crazy mutable APIs. In general notebooks align with other code written by people who aren’t usually software engineers building production systems. They’re much more about getting things done, APIs and tools are less questioned, a lot of pain is swallowed because PhDs have plenty of time to write a few lines of code. I don’t want to sound disparaging towards these people, it’s just a different set of tradeoffs from writing production grade software.

Re: What’s wrong with computational notebooks?

#42

Post by snapetom »

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. Meanwhile, we didn't have anyone that was devoted full time on model productionization.

Sharing data? They had enough problems sharing their notebooks.

Re: What’s wrong with computational notebooks?

#43

Post by chirau »

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…

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 have to go back and do all that. Don't even get me started on the operations you'd have done with those dataframes prior.

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

Re: What’s wrong with computational notebooks?

#44

Post by wwarner »

I have been heads down in jupyter for the past couple of weeks and I finally realized I just DO NOT LIKE IT AT ALL! Cracks started appearing and then suddenly there was an avalanche of disappointment.

The first crack -- it's almost impossible to build a nice presentation in Jupyter, because you always have to show your code and its stderr. I imported all the TeX goodness, and it looked pretty nice, but I couldn't show the output without showing the TeX code. Importing the TeX interpreter is quite non-standard and means that my notebook doesn't play well with the public servers. I also got burned by some kind of permissions issue, so that all my charts ended up being invisible to read-only users.

The second crack -- I can only look at the code from within my own jupyter server. The source is buried in a very noisy json format.

The third crack -- Who wants to write code in the impoverished browser based editor provided? How many times have I deleted a closing brace that was automatically inserted incorrectly? How can I do a global search and replace?

The fourth crack -- I can't test my code unless I include all the tests in the notebook!

I'm complaining. I realize that I don't have anything constructive to offer, and I'm really a beginner. However, I think some of my disappointment is justified, as I think it was reasonable to assume that I could build my notebooks to be next level presentations.

Re: What’s wrong with computational notebooks?

#45

Post by mikepurvis »

wwarner wrote: post #44

I have been heads down in jupyter for the past couple of weeks and I finally realized I just DO NOT LIKE IT AT ALL ! Cracks started appearing and then suddenly there was an avalanche of disappointment. The first crack -- it's almost impossible to build a nice presentation in Jupyter, because you always have to show your code and its stderr. I imported all the TeX goodness, and it looked pretty nice, but I couldn't sh…

This all sounds very familiar to me. I'm at a robotics company; we had some experimental infrastructure built up around processing ROS bag files via notebooks, and it just eventually became like pulling teeth. Stuff would get cut and pasted between notebooks, or moved out to helper modules which then had versioning and permissions chaos. Each bag needed its own notebook/interpreter instance because there's no way to rerun a notebook on new data, but then the server would explode because of these massive Python processes hanging around with half-processed data state still in them.

In the end we dumped it all and turned the good parts into a sane CLI tool which ingests data and dumps out Bokeh plots. At some point we'll throw a Jenkins front end on it, but the current approach seems to be working fine.

Re: What’s wrong with computational notebooks?

#47

Post by tgb »

sillysaurusx wrote: post #37
IanCal wrote: post #19

Earlier quoted context omitted.

If people are wondering about cases that can cause this - a common one (for me) is a mis-spelled variable name. If you go back and change it, the old one is still there and if you make the same mistake twice you will have code that runs but doesn't work. It's then really not obvious why it doesn't work.

It's best to think of the notebook as a REPL. So you'd want to run `del foo` on the old name. In fact, this is a good counterexample. Why should the notebook delete the old variable name? What if its value is a thread currently executing? Notebooks are REPLs, and it's better to get used to that than to try to enforce some confusing time traveling.

But, strangely, Jupyter doesn't also give you a REPL (like, say, R Studio does). I'm always making new cells in the middle to output the column names of my spreadsheet, and then I have to delete them. I used to just always have an ipython REPL running and test things out in there as I write. You can start a ipython instance on the same kernel but I found that messed up my plots when I did that IIRC.

Re: What’s wrong with computational notebooks?

#48

Post by LifeIsBio »

I love jupyter notebooks. Without them, I wouldn’t have been half as productive as I was during my PhD.

Here’s a post I wrote just a few weeks ago describing some of the conventions that I established for myself over the course of 5 years:

https://jessimekirk.com/blog/notebook_rules/

I suspect that a lot of the conventions I describe help mitigate problems described here, some of which should be strictly or optionally enforced by the notebook instead of the user.

(The site’s very much a work in progress, so expect to see odd and broken things if you go poking around.)

Re: What’s wrong with computational notebooks?

#49

Post by mistrial9 »

rb808 wrote: post #14

I tried to encourage our team to use notebooks, however everyone prefers using PyCharm and git for sharing code. We dont have much visualization, which might be the reason, but I was surprised just how many people just hated it.

Notebooks are not so much for writing programs or collections of functions.. they are better for a style of "code plus explanation" .. add flexible inline charting for data itself

Re: What’s wrong with computational notebooks?

#50

Post by antipaul »

sillysaurusx wrote: post #37
IanCal wrote: post #19

Earlier quoted context omitted.

If people are wondering about cases that can cause this - a common one (for me) is a mis-spelled variable name. If you go back and change it, the old one is still there and if you make the same mistake twice you will have code that runs but doesn't work. It's then really not obvious why it doesn't work.

It's best to think of the notebook as a REPL. So you'd want to run `del foo` on the old name. In fact, this is a good counterexample. Why should the notebook delete the old variable name? What if its value is a thread currently executing? Notebooks are REPLs, and it's better to get used to that than to try to enforce some confusing time traveling.

Agree. Get used to the habit of deleting old objects/names when you are replacing them, if you work in notebooks
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