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GitHub and Jupyter IPython Notebooks

199 pointsby benn_88about 10 years ago

20 comments

RogerLabout 10 years ago
I am utterly giddy about this. I&#x27;ve spent a lot of time in the book I am writing to generate PDFs, to create TOCs for links to nbviewer, managing all these links and production every time I made a change. Now people can just view it directly in github. Life is as it should be.<p>There is just so much innovation and hard work coming out of this group, which is quite tiny. Any time I&#x27;ve raised an issue, even if it turned out to be my own dumb fault, gets the immediate attention and support of a core developer.<p>If you want to communicate with programmers there really isn&#x27;t a better platform out there. The old &#x27;write code, run code, save results, write latex, gen document, find error, repeat, opps code is out of sync with results....&#x27; is pining for the fjords.
jlrkabout 10 years ago
Yes! A million times, yes! This lowers the barrier to sharing research results stored in a private repo with collaborators. Also, for those who have been looking for ways to display equations in markdown[1], you can embed the equations in markdown (Ipython uses Mathjax) within the notebook.<p>[1] <a href="https:&#x2F;&#x2F;github.com&#x2F;github&#x2F;markup&#x2F;issues&#x2F;274" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;github&#x2F;markup&#x2F;issues&#x2F;274</a>
mvermaatabout 10 years ago
This is great! We use IPython Notebook a lot in our group, for exploratory data analysis, teaching, sharing experimental results, and as an electronic lab notebook. Inline GitHub rendering is very nice for all our public work.<p>If you run a private GitLab server, you could have a look at my patch which adds similar functionality to GitLab (in a rather ad-hoc way): <a href="https:&#x2F;&#x2F;gist.github.com&#x2F;martijnvermaat&#x2F;6926070" rel="nofollow">https:&#x2F;&#x2F;gist.github.com&#x2F;martijnvermaat&#x2F;6926070</a>
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Myrmornisabout 10 years ago
This is amazing. I think ipython notebook is fantastic in all regards. However, I feel there&#x27;s a bit of an elephant in the room. The main tools I use as a programmer are shell and a text editor. I&#x27;m not about to start writing code in a web browser[1]. Is there any hope that there will be a good workflow for somehow editing .ipynb from a text editor or is that antithetical to the design? Could markdown perhaps be used as a primary editing format to target ipynb?<p>Looks like there&#x27;s at least one project doing that. <a href="https:&#x2F;&#x2F;github.com&#x2F;aaren&#x2F;notedown" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;aaren&#x2F;notedown</a><p>And there&#x27;s the emacs-specific project <a href="https:&#x2F;&#x2F;github.com&#x2F;tkf&#x2F;emacs-ipython-notebook" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;tkf&#x2F;emacs-ipython-notebook</a><p>[1] EDIT: I mean, not right now anyway. I&#x27;ve got a feeling that statement could seem a bit dated later in my life...
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munroabout 10 years ago
So weird, I was playing with IPython Notebook with PyCharm yesterday. Then I went on to think about how it could be integrated into Github without building the compiled files into the repo. :)<p>Really there&#x27;s no solution for extending Github except wait for them to integrate hooks. It would be nice if they made this more generic, and created a file render hook, that would allowed devs to render whatever types of files they want into Github Markdown.
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bigredhdlabout 10 years ago
Just a general comment, but in my opinion IPython&#x2F;Jupyter is worth learning Python for. It is such a great platform for tinkering with data or really any idea you might play with in code.
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rcptabout 10 years ago
Hey this is great! I just took a look and saw that a notebook [1] I was tracking in github is now rendering beautifully - and I didn&#x27;t have to do anything!<p><a href="https:&#x2F;&#x2F;github.com&#x2F;rcompton&#x2F;ml_cheat_sheet&#x2F;blob&#x2F;master&#x2F;supervised_learning.ipynb" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;rcompton&#x2F;ml_cheat_sheet&#x2F;blob&#x2F;master&#x2F;super...</a>
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batbombabout 10 years ago
There&#x27;s a new problem which still hasn&#x27;t been resolved w.r.t. iPython notebooks and reproducible results, and that&#x27;s the problem of private, ephemeral, or mutable data. At the very least, iPython theoretically helps with the audit trail for private and mutable data, but it doesn&#x27;t necessarily foster (re)producible results or alternative analysis.<p>This is a more general problem overall, but potentially something like magnet URIs and bittorrent could really help with part of the problem. (I don&#x27;t really believe git as a system nor GitHub as a platform to be the appropriate place to solve this either).
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Fomiteabout 10 years ago
This also means, at GitHub repos can get DOIs via FigShare, you can have DOIs for an iPython Notebook, which is <i>awesome</i>.
sabootabout 10 years ago
Okay, what is the best format to store images in? My notebooks contain lots of graphs and output but I&#x27;d rather avoid saving the raw pixels. So far I&#x27;ve been using SVG with mixed success. Does anyone use anything else to save space?
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stevetjoaabout 10 years ago
Great idea! Although it appears that the Audio widget does not display correctly. Compare:<p><a href="http:&#x2F;&#x2F;nbviewer.ipython.org&#x2F;github&#x2F;stevetjoa&#x2F;stanford-mir&#x2F;blob&#x2F;master&#x2F;notebooks&#x2F;onset_detection.ipynb" rel="nofollow">http:&#x2F;&#x2F;nbviewer.ipython.org&#x2F;github&#x2F;stevetjoa&#x2F;stanford-mir&#x2F;bl...</a><p><a href="https:&#x2F;&#x2F;github.com&#x2F;stevetjoa&#x2F;stanford-mir&#x2F;blob&#x2F;master&#x2F;notebooks&#x2F;onset_detection.ipynb" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;stevetjoa&#x2F;stanford-mir&#x2F;blob&#x2F;master&#x2F;notebo...</a>
huacabout 10 years ago
Hope support for R-markdown is next!
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shepardrtcabout 10 years ago
So they&#x27;re only displaying the notebooks, but not actually allowing you to work in them, right? Because for a minute there I was pretty excited!
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cabhishekabout 10 years ago
Very thoughtful and awesome. Now is there an easy way to save notebooks directly on GitHub?(git as storage system?). That would make the whole flow seamless and make sharing and versioning easy :)
yes_or_gnomeabout 10 years ago
Screen has both &#x27;c&#x27; and &#x27;C-c&#x27; set to new window by default. tmux only has &#x27;c&#x27; by default.<p>From <a href="https:&#x2F;&#x2F;www.gnu.org&#x2F;software&#x2F;screen&#x2F;manual&#x2F;html_node&#x2F;Default-Key-Bindings.html" rel="nofollow">https:&#x2F;&#x2F;www.gnu.org&#x2F;software&#x2F;screen&#x2F;manual&#x2F;html_node&#x2F;Default...</a>:<p><pre><code> C-a c C-a C-c (screen) Create a new window with a shell and switch to that window. See Screen Command. </code></pre> Edit: d&#x27;oh. I had to reread the original comment. You already know this, but by adding &#x27;C-c&#x27; I don&#x27;t have to release the Ctrl button.<p>You can add this to tmux.conf to get screen-like behavior:<p><pre><code> # New Window bind C-c new-window</code></pre>
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agrothbergabout 10 years ago
It would still be nice if IPython Notebook had an option to save the code separate from the output, for example as two files in the same directory. This would make source controlling easier.
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vhost-about 10 years ago
I just started using these for my data science work and it has been absolutely awesome. Even better now that they display on Github and apparently (based on a comment below) Gitlab too.
andersonfreitasabout 10 years ago
Would be nice to have .ipynb preview on Gist also!
calebmabout 10 years ago
This is awesome! Similar to nbviewer.ipython.org functionality.
bruce487about 10 years ago
Awesome, thanks for sharing.