Learning about ‘nbdev’ while building a Python package for PDF machine learning datasets

Some early thoughts on the benefits and possible drawbacks of using fastai’s ‘nbdev’ literate programming tool which is a suite of tools that allows you to Python software packages from Jupyter notebooks.

Alex Strick van Linschoten


January 6, 2022

While working to develop a computer vision model that detects redactions in documents obtained as a result of FOIA requests, I have encountered some tasks that I end up repeating over and over again. Most of the raw data in the problem domain exists in the form of PDFs. These PDF files contain scanned images of various government documents. I use these images as the training data for my model.

The things I have to do as part of the data acquisition and transformation process include the following:

It’s not hard to see that many of these things likely apply to multiple machine learning data acquisition scenarios. While writing the code to handle these elements in my specific use case, I realised it might be worth gathering this functionality together in an agnostic tool that can handle some of these scenarios.

I had wanted to try out nbdev ever since it was announced back in 2019. The concept was different to what I was used, but there were lots of benefits to be had. I chose this small project to give it an initial trial run. I didn’t implement all of the above features. The two notable missing parts are text extraction and data versioning and/or synchronisation.

pdfsplitter is the package I created to scratch that itch. It’s still very much a work in progress, but I think I did enough with nbdev to have an initial opinion.

I think I had postponed trying it out because I was worried about a steep learning curve. It turned out that an hour or two was all it took before I was basically up and running, with an understanding of all the relevant pieces that you generally use during the development lifecycle.

Built in to nbdev in general is the ability to iterate quickly and driven by short, small experiments. This is powered by Jupyter notebooks, which are sort of the core of everything that nbdev is about. If you don’t like notebooks, you won’t like nbdev. It’s a few years since it first saw the light of day as a tool, and as such it felt like a polished way of working, and most of the pieces of a typical development workflow were well accounted for. In fact, a lot of the advantages come from convenience helpers of various kinds. Automatic parallelised testing, easy submission to Anaconda and PyPi package repositories, automatic building of documentation and standardising locations for making configuration changes. All these parts were great.

Perhaps the most sneakily pleasant part of using nbdev was how it encouraged best practices. There’s no concept of keeping test and documentation code in separate silos away from the source notebooks. Following the best traditions of literate programming, nbdev encourages you to do that as you develop. Write a bit of code here, write some narrative explanation and documentation there, and write some tests over there to confirm that it’s working in the way you expected. When Jeremy speaks of the significant boost in productivity, I believe that a lot of it comes from the fact that so much is happening in one place.

While working on pdfsplitter, I had the feeling that I could just focus on the problem at hand, building something to help speed up the process of importing and generating images from PDF data for machine learning projects.

Not everything was peaches and roses, however. I ran into a weird mismatch with the documentation pages generated and my GitHub fork of nbdev since I was using main as the default branch but nbdev still uses master. I will be submitting an issue to their repository, and it was an easy fix, but it was confusing to struggle with that early on in my process. I’m also not sure how well nbdev will gel with large teams of developers, especially when they’re working on the same notebooks / modules. I know reviewnb exists now and even is used within fastai for code reviews, but I would imagine an uphill battle trying to persuade a team to take a chance with that.

I’ve been using VSCode at work, supercharged with GitHub Copilot and various other goodies, so it honestly felt like a bit of a step back to be forced to develop inside the Jupyter notebook interface, absent all of my tools. I also found the pre-made CLI functions a little fiddly to use — fiddly in the sense that I wish I’d set up some aliases for them early on as you end up calling them all the time. In fact, any time I made a change I would find myself making all these calls to build the library and then the documentation, not forgetting to run the tests and so on. That part felt a bit like busy work and I wish some of those steps could be combined together. Maybe I’m using it wrong.

All in all, I enjoyed this first few hours of contact with nbdev and I will continue to use it while developing pdfsplitter. The experience was also useful to reflect back into my current development workflow and environment, especially when it comes to keeping that close relationship between the code, documentation and tests.

[Photo by Laura Ockel on Unsplash]