Compatibility between Jupyter Notebooks / Binder and DAR / Texture / Stencila

Question

Compatibility between Jupyter Notebooks / Binder and DAR / Texture / Stencila

Closed this issue 2 years ago · 16 comments

[ Project Contact ] @minrk, @nuest
[ GitHub Repo ] https://github.com/minrk/jupyter-dar
[ Track ] Openness,
[ Location ] Cambridge UK, BST
[ Coach ] @chadsansing

Description

Binder is an online service for running Jupyter Notebooks and other environments. Texture/Stencila are editors for reproducible research documents. We want to connect them so that users can edit reproducible documents (DAR files) as part of a binder project.

Objectives:
Understanding DAR
Launching Stencila Editor on Binder (potentially not launching anything else, i.e. w/o the Jupyter Notebook start page)
repo2docker support for DAR files

Want to contribute to this project during #mozsprint?

Join us at the Global Sprint, May 10-11. Leave a comment below if you're interested in contributing to this project during #mozsprint 2018!

Note to the Project Lead 🎉

Congrats, @minrk, nuest! This is your official project listing for the Mozilla Global Sprint 2018. To confirm your registration, please complete and check off the following:

Complete Open Leadership 101
Provide a GitHub repository for work and discussion on your project (in a comment or at the top of this issue)
Create a README file in your project repository. This file should help newcomers understand what your project is, why it's important, and kinds of help you're looking for.
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Turn on your Issue Tracker and create at least three issues to describe each task that you need help with and how a contributor can get started on that task.
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If you get stuck at any point, feel free to look at the requirements page and project templates or reach out to your Project Coach, @chadsansing. We're here to help you through this process.

Answer 1 · 2018-05-10T16:43:18.000Z

🎉 First demo works!

Answer 2 · 2018-05-11T08:13:46.000Z

The project had some world-wide contribution. "Over night" the Stencila devs (@nokome) worked on running Jupyter contexts and contributed some code: minrk/nbstencilaproxy#5

Read more at the Stencila Community: https://community.stenci.la/t/stencila-in-binder/142

And here is the direct link to a working example: https://mybinder.org/v2/gh/nokome/jupyter-dar/add-stencila-host?urlpath=%2Fstencila%2F

Answer 3 · 2018-05-11T08:38:59.000Z

Since @stencila people are now helping out, chat about the project takes place at https://gitter.im/stencila/stencila

Answer 4 · 2018-05-11T10:45:53.000Z

I am currently trying to get the R context working... found a mismatch in confguration file paths (see stencila/r#22) and the RContext is listed in Stencila

and errors are gone, but the code is not evaluated yet...

The error is

[E 10:39:53.361 NotebookApp] 500 POST /stencila-host/RContext (172.17.0.1) 6.96ms referer=http://localhost:8888/stencila/?archive=r-markdown

Answer 5 · 2018-05-11T13:15:14.000Z

Status report

We have stopped working on getting R to work - see minrk/nbstencilaproxy#9 (but did find a bug too: stencila/r#22); we need help from the Stencila experts for that, but there's other stuff to do...
@nuest works on packaging the proxy as a proper Python module, which will make installation and maintenance easier down the road (base on https://github.com/jupyterhub/nbrsessionproxy)
@minrk works on getting https://github.com/jupyter/repo2docker ready to handle repos with Dar archives - the Docker image generation will be like magix 🦄

Answer 6 · 2018-05-11T13:29:17.000Z

The Python module for the proxy also allows us to extend the Jupyter landing page with a nice button (minrk/nbstencilaproxy#1):

Answer 7 · 2018-05-11T14:53:51.000Z

Demo works (on an inofficial binder website) 🎉 💯

Try it at http://binder.minrk.net/v2/gh/minrk/jupyter-dar/master?urlpath=%2Fstencila%2F

Answer 8 · 2018-05-14T13:28:03.000Z

@nuest many thanks for documenting your progress here, it's fab to have this record and all the links 💯

Answer 9 · 2018-10-24T20:48:04.000Z

The software is ready for this to work on mybinder.org, we're working on some examples and a wrap-up blog post, see minrk/nbstencilaproxy#12

Answer 10 · 2018-11-05T18:08:11.000Z

@chadsansing If you're still "coaching" this, feedback on a wrap-up blog post is very welcome: minrk/nbstencilaproxy#12 (comment)

Answer 11 · 2018-11-20T09:50:30.000Z

The wrap-up blog post is now online at

https://elifesciences.org/labs/d42fe2b9/integrating-binder-and-stencila-the-building-blocks-to-increased-open-communication-and-transparency

Some cross-posts will happen during the coming days, see minrk/nbstencilaproxy#12 for links.

Answer 12 · 2018-11-20T13:09:50.000Z

Fantastic read, I learnt so much about what actually happened with this project and what each of you did (although not all technical details absorbed, but that's ok for me 😄). Thank you!! 💯

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