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Author
Last Commit
Sep. 22, 2018
Created
Aug. 10, 2017

Build Status Join the chat at https://gitter.im/iodide-project/iodide


The Iodide notebook

Try it in your browser right now! (More examples)

Please note: Iodide is in early alpha, and still subject to breakage, changes, and overhauls

View source for science

Today, sharing scientific results is easier than ever. You can email a PDF, write up a Google doc, or post to your blog. You can embed plots, data tables, and even interactive visualizations. But what if you want people to be able to replicate and extend your results -- to take your results and “view source” to see how you arrived at your conclusions? Or even hack and remix them to ask their own questions?

To do that now, you typically have a couple options. You could send your code along side your nice, clean PDF or HTML export, allowing you fine-grained control over your presentation, but requiring you to separate your presentable results from your code and to manage multiple files. Alternatively, you could share your results and code bundled together in a notebook format that mixes code with write-up; this has the advantage of keeping your code and results closely tied together, but the presentation can get a bit unwieldy, especially if you want to share your results with a less technical audience. And in either case, sharing your code will only allow your collaborators to replicate and extend your results if they are first able to replicate your whole setup -- if they can run your code with the same libraries, the same data, and the server access.

If only there was a technology that was great for presenting documents and visualizations, that allows code to run anywhere with zero setup, and that all scientists and citizens had access to...

Luckily, that technology already exists: the web browser.

Iodide is a modern, literate, and interactive programming environment that uses the strengths of the browser to let scientists work flexibly and collaboratively with minimal friction. With Iodide you can tell the story of your findings exactly how you want, leveraging the power of HTML+CSS to display your results in whatever way communicates them most effectively -- but still keeping the live, editable code only one click away. Because Iodide runs in the browser you already have, you can extend and modify the code without having to install any software, enabling you to collaborate frictionlessly.

And thanks to WebAssembly, working in the browser does not mean that you have to work in Javascript. We're already working on getting Python+Numpy+Pandas running in the browser, and that's just the start. We envision a future workflow that allows you to do your data munging in Python, fit a quick model in R or JAGS, solve some differential equations in Julia, and then display your results with a live interactive d3+Javascript visualization... and all that within within a single, portable, sharable, and hackable file.

Our focus is on delivering frictionless, human-centered tools to scientists. You can read more about our core principles below; if our vision resonates with you, please consider contributing to the project!

PS: We're working on a few other ways of making this in-browser workflow as ergonomic for scientific tasks as possible. Two of those key efforts will be (1) using modern JS transpilation tools to extend JS syntax just enough for matrix notation, broadcasting, and other basic scientific computing needs; and (2) compiling best-in-class C/C++ science libraries (and runtimes!) to Webassembly and wrapping them in ergonomic JS APIs. If either of those projects appeals to you, please reach out!

Get in touch

Please feel free to join our Google group to contact us and keep up with what we're working on.

You can also chat with us on Gitter.

Setup

Run npm install after cloning this repository.

Running/Building

Client-only mode

If you're only working on client code and don't need to use/test any of the server functionality described below. You can use npm run start-and-serve to write development versions of the Iodide client-side app resources to dev/ and to serve the files in that folder at http://localhost:8000. You can open http://localhost:8000/iodide.dev.html in your browser to get started with a blank notebook, or open http://localhost:8000 to see the list of files saved in dev/ (in case you have exported other test notebooks in that folder)

The command npm run start-and-serve runs in watch mode, so changes to files will be detected and bundled into dev/ automatically, but you will need to refresh the page in your browser manually to see the changes -- we have disabled "hot reloading" because automatically refreshing the browser would cause any active notebooks to lose their evaluation state.

If you require verbose Redux logging, you can use the command npm run start-and-serve -- reduxVerbose

Exporting from client-only dev mode

In this mode, resource paths are set to be relative to the dev/ directory. Thus, if you export a bundled notebook from a dev notebook, you need to be sure save the exported HTML file in the dev/ folder for the relative paths to correctly resolve the required js, css, and font files (and if you want to share a notebook that you created in a dev environment, you'll need to update the paths to point to the web-accessible resources at iodide.io and iodide.app).

Server mode

We have been building an experimental iodide server based on Python and Django. Currently the main features it supports are login/identity (via the github API). To test/run it locally, follow this set of steps:

On subsequent runs, you only need to run make up.

Additionally, if you are working on client code, you can run npm run start in a separate terminal to run webpack in watch mode (which will make your client code changes visible on page reload). If you require verbose Redux logging, you can set the environment variable REDUX_LOGGING=VERBOSE with the command REDUX_LOGGING=VERBOSE npm run start

Testing

Run npm test to run the test suite once, or npm test --watch to run the suite in watch mode, which will automatically re-run the tests when the source or tests have changed.

Using the notebook

Visit our examples repo at https://github.com/iodide-project/iodide-examples to see demo notebooks

For now, work can be saved to local storage using the "Save Notebook " menu item, or exported with "Export Notebook ", which allows you to download your work as HTML file that will run anywhere (for the time being, we advise periodically exporting any code you care about).

We've modeled much of the experience on Jupyter as our jumping-off point, with a few additions. Check out our milestones & issues to see the direction we're going.

Contributing

Please join us! The notebook is written using React+Redux, which, if you haven't used them, are pretty delightful -- there's some learning curve, but even for non-professional webdevs the curve is not too steep, and the mental model is clean and powerful.

See our "How to Contribute" page for more information.

We especially need help with:

  • test coverage for everything in our system.
  • demos, tutorials, and documentation. The more we have, and the better organized it is, the better.

Our core principles

  • Human factors come before everything else
  • Scientific computing and computational inquiry implies different needs than typical software development
  • We want to make the advantages of web tech available to scientists without requiring them to become fully fledged web devs

Secondary principles

Flowing from those core principles, we have a number of secondary principles/objectives that revolve around the notion of reduce friction for people that want out the platform.

  • Portability is key -- users should be able to get up and running immediately and be able to start doing real work entirely within the browser.
    • Allowing the notebook to work with other client and/or server-side programs/components/tools (e.g. external editors, external compute kernels (other languages or big data thingies)) might be something cool to work on down the road, but is not an objective at the moment
    • Addons to do things that the browser restricts or can’t do for some reason (file system access, halting hung scripts) could potentially be ok for power users, but cannot be a requirement to get going with a satisfactory experience.
  • No magic APIs -- users should (within reason) not have to learn about a ton of idiosyncrasies of the notebook to get up and running.
    • Users need to be able to build off of existing work/examples/resources. Users need to be able to pull examples from bl.ocks.org or JSfiddle or Stackoverflow and have them run in the notebook without modification (within reason). This means, among other things, seamless access to all browser APIs is a hard requirement.
    • Helper libraries are desirable, but they should just act like regular JS libraries and not require users to contort their mental model of how vanilla JS works, or pollute the regular JS environment. (Ex: it would be preferable to add a single namespaced helper lib than to dump a bunch of utility functions into the global scope).
    • We want to support syntax extensions for mathematics, but we want them to be opt in, not something that a user will have to learn to be able to use a notebook.
  • Don’t innovate too much -- at least initially, we want to follow existing, familiar paradigms that will enable people to dive right in.

You can read more about how these priciples have shaped the choices we've made so far in our FAQ

Initial use case

In building this tool, we will keep our eyes on a broad swath of computational inquiry use cases, and we’ll strive to avoid making decisions that limit the tools use to a specific domain. We're initially be targeting small to medium N data science workflows, since these often come up at Mozilla and we're very familiar with them, but if your use case requires something that we haven't addressed yet, please leave us a message at our Google group.

Roadmap

There are a bunch of features that we know we want to build to make this compelling. Here are a few in rough order of priority:

  • Export improvements
    • Option to Inline bundle.js (rather than load from URL)
    • Options to inline external libs in a saved snapshot
    • Saving an “environment” (a la R and R Studio) with selected variables that were computed during a session
      • serializing/compressing data inline (needed for bigger datasets),
      • Estimate of total bundled size with all scripts and environment vars
    • Export/import to gists, g-drive, dropbox, and other external repos
  • r-studio mode (direct editing of jsmd)
  • editor improvements
    • Code editor
      • Special character insertion (greek, special operators, etc)
    • Latex editor
      • hints, autocomplete (for latex, this includes special character insertion)
      • Lyx-like wysiwyg preview for equation editing
  • UI for importing local data from file (with drag and drop? Needed for XSS reasons, lack of filesystem access reasons)

License

The Iodide code is shared under the terms of the Mozilla Public License v2.0. See the LICENSE file at the root of the repository.

Latest Releases
v0.6-alpha
 Sep. 6 2018
v0.6-alpha
 Aug. 30 2018
single-frame
 Aug. 9 2018
pyodide-20180623
 Jun. 22 2018
pyodide-20180605
 Jun. 4 2018