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I'm sorry, slight rant, but I do not think notebooks are good for a completed piece of software. Maybe it's good for development/brainstorming but once you are

by foxes 7y ago

I'm sorry, slight rant, but I do not think notebooks are good for a completed piece of software. Maybe it's good for development/brainstorming but once you are done the code needs to be extracted into a more traditional format. In research I have seen countless mathematica/python notebooks which have been released into the wild, and they are all over the place. Maybe software developers will structure it better, but I'm kind of sick of seeing an incoherent spaghetti state. Especially since there is no strict ordering of the evaluation of cells. Maybe it would be nice if notebooks could break from the traditional "page of working" format. It could display as some tree/graph which orders the state/dependency in evaluation. Otherwise it needs an "export" button.

conradludgate 7y ago
nbdev has exactly that export functionality. https://nbdev.fast.ai/export/ https://nbdev.fast.ai/export/
dr_zoidberg 7y ago
What you complain about is more about the author of the notebook being disorganized rather than the format. The format also allows that to happen, but it's a lack of discipline on the author that creates that mess. Many people don't care about reproducibility, or having a paper that can be simply read and understood. They just care about getting their paper out. Part to blame is also on the reviewers who don't really evaluate this as part of the paper (assuming they're given access and the opportunity to evaluate the code, that is!). I recently reviewed a paper for a conference and it was a mess in every aspect. I wish they had included the .ipynb file. Instead, they provided mangled (both by cropping and jpeg compression) screenshots of the notebook. The code was an utter mess (instead of doing X_prime = X[10:100], they did X_prime = [X[10], X[11], X[12], ..., X[98], X[99]]). I gave that mess the strong reject it deserved (the rest of the paper was on par with the code, if not worse). I'm still waiting to see if the other reviewes will do the right thing, or they'll jump on the fad that """deep learning""" (they used 90's machine learning methods at best) has become.
- dr_zoidberg 7y ago
  Since I can't edit, I'll reply to myself: The other reviewers are on the deep learning fad train. The paper has been accepted, despite being a big pile of nonsense.

by foxes 7y ago

conradludgate 7y ago

nbdev has exactly that export functionality. https://nbdev.fast.ai/export/ https://nbdev.fast.ai/export/

dr_zoidberg 7y ago

What you complain about is more about the author of the notebook being disorganized rather than the format. The format also allows that to happen, but it's a lack of discipline on the author that creates that mess. Many people don't care about reproducibility, or having a paper that can be simply read and understood. They just care about getting their paper out. Part to blame is also on the reviewers who don't really evaluate this as part of the paper (assuming they're given access and the opportunity to evaluate the code, that is!). I recently reviewed a paper for a conference and it was a mess in every aspect. I wish they had included the .ipynb file. Instead, they provided mangled (both by cropping and jpeg compression) screenshots of the notebook. The code was an utter mess (instead of doing X_prime = X[10:100], they did X_prime = [X[10], X[11], X[12], ..., X[98], X[99]]). I gave that mess the strong reject it deserved (the rest of the paper was on par with the code, if not worse). I'm still waiting to see if the other reviewes will do the right thing, or they'll jump on the fad that """deep learning""" (they used 90's machine learning methods at best) has become.

dr_zoidberg 7y ago
Since I can't edit, I'll reply to myself: The other reviewers are on the deep learning fad train. The paper has been accepted, despite being a big pile of nonsense.