Jupyter, Mathematica, and the Future of the Research Paper • Hacker News Board

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

#171

Post by _Wintermute » Mon, Apr 16, 2018, 6:41 AM UTC

gaius wrote: post #73

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…

combine several languages in a single document without any issues You can do this with RMarkdown as well, despite the name, and run notebooks in RStudio. Much better experience than Jupyter in a browser. https://yihui.name/knitr/demo/engines/

RMarkdown is pretty useless if you're not using R.

  Except engine='R' (default), all chunks are executed in separate sessions, so the variables cannot be directly shared.

So yes you can write a python snippet, but good luck trying to write a notebook.

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

#172

Post by infinite8s » Mon, Apr 16, 2018, 3:07 PM UTC

carreau wrote: post #161

recharged96 wrote: post #155

Earlier quoted context omitted.

It's not free. Grant money means someone's paid for it (us, taxes). Volunteer is about credit, not fiat, but still costs something (gpl restrictions). Jupyter is great, it's revolutionized online education for example. But it's not as full featured as Mathematica, and like most Foss projects, slower to fix bugs, aka you get what you pay for. Both have a place unless you have hired, 100% dedicated help on juptyer. Thi…

Grant usually differ from US taxes. And AFAICT, Jupyter received no money from govt source. Jupyter is not GPL but MIT, and volunteering is rarely about credit.

I'm pretty sure some of Fernando's early work on ipython was funded through his NSF grants.

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

#173

Post by currymj » Mon, Apr 16, 2018, 3:08 PM UTC

ChrisRackauckas wrote: post #116

currymj wrote: post #82

Earlier quoted context omitted.

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 receiv…

https://www.youtube.com/watch?v=jxl6IvDvGHU

That's a video where they lay out how they want it to work, if you're interested and haven't seen it.

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

#174

Post by littlehood » Mon, Apr 16, 2018, 4:56 PM UTC

ChrisRackauckas wrote: post #168

littlehood wrote: post #160

Earlier quoted context omitted.

You asked for that block in the second question. You sound very entitled to answers.

I am just curious what led him to his conclusions. He made a very nasty comment about a group of people and gives no justification for why. I cannot seem to find out why when Googling either. Is it not okay to ask someone how they came to their conclusions?

You could've asked politely, but it looks you missed your chance.

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

#175

Post by goerz » Mon, Apr 16, 2018, 6:03 PM UTC

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…

> Plus, you get to use a proper text editor instead of editing on a browser textarea

I have a shortcut that lets me edit any browser text area in MacVim, which works out really well in the Jupyter notebook.

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

#176

Post by emj » Tue, Apr 17, 2018, 9:40 AM UTC

abhirag wrote: post #84

emj wrote: post #54

Earlier quoted context omitted.

Requiring basic Emacs knowledge is just too much, just looking through the features of org-babel I can't really find anything that makes it better suited. Except not having to bother with a webbrowser, that is a nice plus, but hardly important for most people I work with.

I have used both Jupyter Notebooks and org mode with org-babel extensively and I agree with the OP regrading the fact that the org-babel workflow is vastly superior, OP did point out a few features which org mode workflow has and Jupyter Notebooks don't but I will try and provide a comprehensive list: 1. Plain text format, git and git diffs work 2. You can combine many languages in a single document, and every code b…

I will try to run a org-mode to ipynb converter, so thanks to your suggestion! I just wish there was an Emacs version that wasn't to differnt from everything else so other people could look past the stigma of Emacs. So thank you for the feature run down, and to be cyrstal clear I want more options, but I will only be able to run org-mode/babel myself. Requiring Emacs is just too big of an hurdle for anything bigger than a two man team.

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

#177

Post by abhirag » Tue, Apr 17, 2018, 2:49 PM UTC

emj wrote: post #176

abhirag wrote: post #84

Earlier quoted context omitted.

I have used both Jupyter Notebooks and org mode with org-babel extensively and I agree with the OP regrading the fact that the org-babel workflow is vastly superior, OP did point out a few features which org mode workflow has and Jupyter Notebooks don't but I will try and provide a comprehensive list: 1. Plain text format, git and git diffs work 2. You can combine many languages in a single document, and every code b…

I will try to run a org-mode to ipynb converter, so thanks to your suggestion! I just wish there was an Emacs version that wasn't to differnt from everything else so other people could look past the stigma of Emacs. So thank you for the feature run down, and to be cyrstal clear I want more options, but I will only be able to run org-mode/babel myself. Requiring Emacs is just too big of an hurdle for anything bigger t…

It hurts to hear stigma and Emacs together in a sentence but I guess you are referring to the arcane keybindings of Emacs. In that case I use native keybindings for editing in Emacs i.e. the old Cntrl-C, Cntrl-V, Cntrl-A, Cntrl-Z, Cntrl-S and vim keybindings for executing commands i.e. for things like running code. This is a great setup for beginners so do contact me if you need Emacs to be used with native keybindings :)

Just to give an example of what can be done using org-mode, this is the project I am using to grok Literate Programming -- http://ray_tracer.surge.sh/

The whole thing is generated using one org-mode file -- https://gitlab.com/snippets/1710454

and this org-mode file is the one I work in, it will eventually generate the source code in separate files too, once I have finished the project.

This is what my setup looks like -- https://i.imgur.com/mqi8vPR.png

Anyways I can't convince you to use it, but hopefully I can convince you to give it a try, it isn't easy but it is worth it :)

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

#178

Post by gaius » Tue, Apr 17, 2018, 2:59 PM UTC

spot wrote: post #110

sanderjd wrote: post #47

Earlier quoted context omitted.

I used MathCAD in physics and chemistry classes in college. I frequently wonder what happened to it, because I share your perception that while Jupyter is very nifty, it is hamstrung by the limitations of the browser environment. I'm waiting impatiently for the coming revolution of non-web collaborative internet-connected rich client applications.

> In terms of general usability and experience, 20-years-ago blows away modern-day Jupyter and it’s silly “cells” interface, which it does not because it’s better but because it’s trying to force itself into a web browser. I am really interested in the specific advantages MathCAD had/has, and the problems you see with cells and being in a web browser. > the coming revolution of non-web collaborative internet-connecte…

the problems you see with cells and being in a web browser.

My end goal is a document, and for that I either want a programmer-grade text editor, or a full-featured word processor. Filling in a web form is a terrible way to write a document. My tool of choice at the moment is RStudio - all the interactivity you could possibly ask for, and very easy to edit complex files then render them to a great-looking PDF with the output of my code interspersed with paragraphs of text, footnotes and TOC and all the rest.

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

#179

Post by jonnycomputer » Mon, Apr 23, 2018, 2:55 PM UTC

heisenzombie wrote: post #165

jonnycomputer wrote: post #159

R Studio Notebooks are pretty good too; I like that, by default, there is an interactive console connected to the same kernel in addition to the notebook. This allows me to use the console to interactively probe my data, or try out something, and then record a more finished product in the notebook itself. I think this can be done in Juypter ( http://jupyter-notebook.readthedocs.io/en/latest/examples/No... ), but, not…

In JupyterLab ( http://jupyterlab.readthedocs.io/en/stable/ ), this is built-in. Just right click a notebook and choose "New Console for Notebook". JupyterLab is in beta and is intended to replace the current Jupyter front-end.

I tried JupyterLab out. Definitely an upgrade.