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Jupyter, Mathematica, and the Future of the Research Paper

paulromer.net

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Re: Jupyter, Mathematica, and the Future of the Research Paper

#111

Post by tincholio »

dahart wrote: post #96
tincholio wrote: post #86

Earlier quoted context omitted.

> One of the more compelling reasons to use Jupyter is inline images and plots You can do those in org, since forever. I meant that the files themselves are plain text, which is good for sharing, version control, etc. ipynb files embed images with Base64 encoding, which makes seeing diffs a major PITA. >This is a wierd thing to say. Jupyter has download as .py right in the file menu. Not to mention download as Markdo…

I Agree with all those points. I've used org mode for a few things, but not for python notebooks. I remember seeing a great video a few years back on using python in org mode to make a research notebook. It really made me want to try org mode for literate / notebook style programming. I think it was this one: https://youtu.be/1-dUkyn_fZA It sounds like org mode does not store images inline, since you don't like the b…

BTW, and unrelated to the Jupyter vs. org discussion, you may find this interesting (just came across it earlier today): https://blog.oscarnajera.com/2017/11/git-diff-images-and-pdf...

Re: Jupyter, Mathematica, and the Future of the Research Paper

#112

Post by mfe5003 »

I learned and was fluent with Mathematica early and learned python later. I still run to Mathematica for doing symbolic analysis because there is basically no impedement between my ideas and the keyboard when I am solving that type of problem. I've moved all my numerical analysis to the scipy system since it is a more natural language for those types of problems.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#113

Post by mistermann »

iguy wrote: post #61

Right, Jupyter is nice to have, but this is really over the top nonsense: Jupyter encourages individual integrity; Mathematica lets individuals hide behind corporate evasion I have no idea what he's talking about re PDF export either. I print to PDF all the time, to email people a static document to look at, etc. It works just fine. (Whether you can you make book-quality formatted text easily, I've no idea, never bee…

The writing style is very reminiscent of Ayn Rand.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#114

Post by improbable22 »

henrikeh wrote: post #107
rotorblade wrote: post #59

Earlier quoted context omitted.

Yeah, I guess that is fair. It might just be that it is more or less the furthest way from how I like to work as I can imagine. > Sin[θ] //TraditionalForm //TeXForm Did not know of this. Thanks!

TeXForm automatically applies TradionalForm unless another *Form is applied. So TeXForm[Sin[x]] gives "\sin (x)"

Indeed, sorry! It even says so in the help.

And while I swear I've had rotorblade's problem before, right now "Copy as LaTeX" seems to do this too.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#115

Post by coldtea »

promer wrote: post #101
iguy wrote: post #61

Right, Jupyter is nice to have, but this is really over the top nonsense: Jupyter encourages individual integrity; Mathematica lets individuals hide behind corporate evasion I have no idea what he's talking about re PDF export either. I print to PDF all the time, to email people a static document to look at, etc. It works just fine. (Whether you can you make book-quality formatted text easily, I've no idea, never bee…

iguy, agreed. You have have no idea because you haven't tried.

Defensive much? Still, that fact remains that the profit-motive accusations for them hampering PDF export are unsubstantiated.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#116

Post by ChrisRackauckas »

currymj wrote: post #82
bloaf wrote: post #21

Earlier quoted context omitted.

Re: Speed Mathematica is undergoing a compiler re-vamp, which may change that.

one pretty clearly inspired by Julia's approach, from what I can understand.

Well I think Mathematica has an interesting spot here. If you consider their symbolic language as instead an AST for mathematical functions with tons of available transformations to perform simplifications, then that can allow for a very nice compiled output. Julia, Modelica, TensorFlow, Mathematica, etc. all seem to be heading in this same direction of codifying and then simplifying mathematical structures to receive better runtime code. There's a lot of convergent development going on here.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#117

Post by ChrisRackauckas »

fdej wrote: post #62
ChrisRackauckas wrote: post #19

Earlier quoted context omitted.

It's not, but for most people it may not matter. Mathematica seems to have a much larger set of integrals, differential equations, special functions, etc. that it can recognize. So as much as I dislike the language itself, I do keep Mathematica installed because in many cases SymPy cannot handle the transformation. On the other hand, open source tools are catching up. Part of the SymPy project is SymEngine which is a…

> On the other hand, open source tools are catching up. SymPy is doing nicely, but it's decades behind Mathematica when it comes to symbolic computation. By the way, if you want to invert a symbolic matrix, chances are that generic Gaussian elimination working with symbolic expressions isn't the best algorithm (it might even give wrong answers if zero testing is done incorrectly), and compiled code isn't going to cha…

It was a bunch of small matrices so it worked out well, but that's good to know. For future reference, what library implements these symbolic linalg routines? When I was looking around I could only find LinBox (http://www.linalg.org/) but the barrier to entry was a little high for me to dig in.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#118

Post by iguy »

promer wrote: post #101
iguy wrote: post #61

Right, Jupyter is nice to have, but this is really over the top nonsense: Jupyter encourages individual integrity; Mathematica lets individuals hide behind corporate evasion I have no idea what he's talking about re PDF export either. I print to PDF all the time, to email people a static document to look at, etc. It works just fine. (Whether you can you make book-quality formatted text easily, I've no idea, never bee…

iguy, agreed. You have have no idea because you haven't tried.

In other news, you will be shocked to hear that major journals also don't accept photographs of proofs clearly worked out on the blackboard. Although, to be fair, I have also not tested this myself.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#119

Post by ChrisRackauckas »

williamstein wrote: post #24
zeth___ wrote: post #13

Jupyter isn't a foil for mathematica. It has completely different use cases. The straight one to one fight is between sagemath, or their rebranded cocal site, and mathematica. In terms of ability to do things sagemath is the glue between all the amazing open source math and science software that has been written over the last 50 years. https://cocalc.com/ But in terms of presentation by far the best is org-mode with…

Thanks for mentioning SageMath and CoCalc (I founded both of these projects)! A minor clarification is that CoCalc is not a rebranding of SageMath, but is instead a new web application whose goal is to make it very easy to collaboratively use Sage, Jupyter, LaTeX, Julia, etc. In constract, Sage is a more traditional open source software package, which people install on their own computers. The goal of Sage is to be a…

First of all, thank you for all of your hard work. One thing I am curious about though is how you think you can match the "cohesiveness" of Mathematica. While I am not a big fan of Mathematica the language, there is something gained by a top down approach. The options all seem to have the same names, the display tools tend to compose with new functionality well, the symbolic parts integrate well with the numerical tooling. While the poly-sourcing approach of Sage can definitely excel in the features area (and definitely surpass it in more "esoteric" areas of algebra), I do think that the tools end up with a higher barrier to entry since it's much harder to police syntactic and dependency inconsistencies. I am trying to work out some of these problems of my own and was wondering how you're coping with it.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#120

Post by paultopia »

todd8 wrote: post #92
tincholio wrote: post #50

Earlier quoted context omitted.

As a die-hard Emacs user, I think that org-mode with it's org-babel capabilities blows Jupyter out of the water, and it produces much better, readable output. You can use it with pretty much any language, and combine several languages in a single document without any issues. Besides all this, it's just a plain text format, and you can extract all the code into proper source files for later offline use, too ('tangling…

I share your opinion about the superiority of org-mode as a means to assemble a document out of various pieces. It's not hard to show nicely formatted code, the code's output, the math behind the code and perhaps a graph of the results all in a LaTeX/PDF document and or HTML. All of this can be done with a flat text file that is easy to save as a part of a project under source control. What I wonder is why are Jupyte…

I think of a Jupyter notebook as a REPL with superpowers. I can try code out in real-time and incrementally like a REPL, but when something breaks, the full history is right in front of me, so I can tweak something 10 lines ago and run the entire thing again like with an ordinary source file. It combines the best of both methods of programming.

Seen that way, sharability is just a nice bonus. Yeah, I'd never try to turn anything directly from a jupyter notebook into a serious way of sharing research results---but for a quick and dirty "here's what I did" on a blog or email or something, or to show students, it does the job.

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