# All Posts

## Adding copy buttons to code blocks in Sphinx

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NOTE: This is now a sphinx extension! Thanks to some friendly suggestions, I’ve written this up as a super tiny sphinx extension. Check it out here: https://github.com/choldgraf/sphinx-copybutton

Sphinx is a fantastic way to build documentation for your Python package. On the Jupyter project, we use it for almost all of our repositories.

A common use for Sphinx is to step people through a chunk of code. For example, in the Zero to JupyterHub for Kubernetes guide we step users through a number of installation and configuration steps.

A common annoyance is that there is a lot of copy/pasting involved. Sometimes you accidentally miss a character or some whitespace. So, I spent a bit of time figuring out how to automatically embed a copy button into code blocks. It turns out this is pretty easy!

Here’s what the final result will look like (just hover the code block below)

wow = this_text
is_so = much*more*copyable


To accomplish this we’ll use the excellent clipboard.js which provides the machinery for copying the contents of an HTML element as well as jquery for modifying our built documentation on-demand.

The result will be a Sphinx site with code blocks that display a copy button when you hover over them. You can see how it looks on this very page, which uses a similar method (but is built with Jekyll).

Here’s what you should do:

1. Add the clipboard.js javascript. Create a javascript script called doc/_static/custom.js. In the file, put the following code (see comments for explanation):

 function addCopyButtonToCode(){
// get all code elements
var allCodeBlocksElements = $( "div.highlight pre" ); // For each element, do the following steps allCodeBlocksElements.each(function(ii) { // define a unique id for this element and add it var currentId = "codeblock" + (ii + 1);$(this).attr('id', currentId);

// create a button that's configured for clipboard.js
// point it to the text that's in this code block
// add the button just after the text in the code block w/ jquery
var clipButton = '<button class="btn copybtn" data-clipboard-target="#' + currentId + '"><img src="https://clipboardjs.com/assets/images/clippy.svg" width="13" alt="Copy to clipboard"></button>';
$(this).after(clipButton); }); // tell clipboard.js to look for clicks that match this query new Clipboard('.btn'); }$(document).ready(function () {
// Once the DOM is loaded for the page, attach clipboard buttons
});

2. Add some CSS to make it pretty. Create a custom CSS file called doc/_static/custom.css (or add to one you’ve already got). In the file, put these lines:

/* Copy buttons */
button.copybtn {
webkit-transition: opacity .3s ease-in-out;
-o-transition: opacity .3s ease-in-out;
transition: opacity .3s ease-in-out;
opacity: 0;
position: absolute;
right: 4px;
top: 4px;
}
div.highlight:hover .copybtn, div.highlight .copybtn:focus {
opacity: .3;
}
div.highlight .copybtn:hover {
opacity: 1;
}
div.highlight {
position: relative;
}

3. Link these scripts in your configuration. You need to link your custom JS and CSS scripts, as well as the clipboard.js script so it ships with your site. In your conf.py file, add the following function/lines (or add to one you’ve already got defined).

def setup(app):


And that’s it! Once you clear your Sphinx cache and re-build your site, you should now have buttons that appear when you hover over them, and that copy the text inside when you click them.

## Thanks

Many thanks to this StackOverflow post for the majority of the code that led to this hack!

## Introducing makeitpop, a tool to perceptually warp your data!

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Note: It should go without saying, but you should never do the stuff that you’re about to read about here. Data is meant to speak for itself, and our visualizations should accurately reflect the data above all else.

## Blogging with Jupyter Notebooks and Jekyll using nbconvert templates

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Here’s a quick (and hopefully helpful) post for those wishing to blog in Jekyll using Jupyter notebooks. As some of you may know, nbconvert can easily convert your .ipynb files to markdown, which Jekyll can easily turn into blog posts for you.

## An academic scientist goes to DevOps Days

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Last week I took a few days to attend DevOpsDays Silicon Valley. My goal was to learn a bit about how the DevOps culture works, what are the things people are excited about and discuss in this community. I’m also interested in learning a thing or two that could be brought back into the scientific / academic world. Here are a couple of thoughts from the experience.

## Combining dates with analysis visualization in python

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Sometimes you want to do two things:

## Dates in python

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As a part of setting up the website for the Docathon I’ve had to re-learn all of my date string formatting rules. It’s one of those little problems you don’t really think about - turning an arbitrary string into something structured like a date - until you’ve actually got to do it.

## Matplotlib Cyclers are Great

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Every now and then I come across a nifty feature in Matplotlib that I wish I’d known about earlier. The MPL documentation can be a beast to get through, and as a result you miss some cool stuff sometimes.

## Brainy Jingle Bells

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This is a quick demo of how I created this video. Check it out below, or read on to see the code that made it!

## The bleeding edge of publishing, Scraping publication amounts at biorxiv

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Per a recent request somebody posted on Twitter, I thought it’d be fun to write a quick scraper for the biorxiv, an excellent new tool for posting pre-prints of articles before they’re locked down with a publisher embargo.

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## 5 things I learned at SciPy

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I’ve finally decompressed after my first go-around with Scipy. For those who haven’t heard of this conference before, Scipy is an annual meeting where members of scientific community get together to discuss their love of Python, scientific programming, and open science. It spans both academics and people from industry, making it a unique place in terms of how software interfaces with scientific research. (if you’re interested the full set of Scipy conferences, check out here.

## Could Brexit have happened by chance?

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As a scientist, watching the Brexit vote was a little bit painful. Though probably not for the reason you’re thinking. No, it wasn’t the politics that bothered me, but the method for making such an incredibly important decision. Let me explain…

## The beauty of computational efficiency

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When we discuss “computational efficiency”, you often hear people throw around phrases like $O(n^2)$ or $O(nlogn)$. We talk about them in the abstract, and it can be hard to appreciate what these distinctions mean and how important they are. So let’s take a quick look at what computational efficiency looks like in the context of a very famous algorithm: The Fourier Transform.

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# NIH Fellowship Success Rates

As I’m entering the final years of graduate school, I’ve been applying for a few typical “pre-doc” fellowships. One of these is the NRSA, which is notorious for requiring you to wade through forests of beaurocratic documents (seriously, their “guidelines” for writing an NRSA are over 100 pages!). Doing so ends up taking a LOT of time.

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## Using Craigslist to compare prices in the Bay Area

In the last post I showed how to use a simple python bot to scrape data from Criagslist. This is a quick follow-up to take a peek at the data.

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## Overview

In this notebook, I’ll show you how to make a simple query on Craigslist using some nifty python modules. You can take advantage of all the structure data that exists on webpages to collect interesting datasets.