Literate [Clojure] Programming: Publishing Documentation In Multiple Formats

This blog post is the sixth, and the last, of a series of blog posts about Literate [Clojure] Programming in Org-mode where I explain how I develop my [Clojure] applications using literate programming concepts and principles.

This last post introduce a tool that leverage the side effect of having all the codes neatly discussed: it gives the possibility to automatically generate all different kinds of project documentation with a single key-binding. The documentation that we will generate are:

  1. Human readable HTML general project documentation
  2. Programming API documentation
  3. Book style complete project documentation in PDF

This series of blog posts about literate [Clojure] programming in Org-mode is composed of the following articles:

  1. Configuring Emacs for Org-mode
  2. Project folder structure
  3. Anatomy of a Org-mode file
  4. Tangling all project files
  5. Publishing documentation in multiple formats (this post)
  6. Unit Testing

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Literate [Clojure] Programming: Tangle All in Org-mode

This blog post is the fifth of a series of blog posts about Literate [Clojure] Programming in Org-mode where I explain how I develop my [Clojure] applications using literate programming concepts and principles.

This new blog post introduce a tool that is often necessary when developing literate applications using Org-mode: the tangle all script. As I explained in a previous blog post, doing literate programming is often like writing: you write something, you review and update it… often. This means that you may end-up changing multiple files in your Org-mode project. Depending how you configured you Emacs environment and Org-mode, you may have missed to tangle a file you changed that may cause issues down the road. This is the situation I will cover in this post.

This series of blog posts about literate [Clojure] programming in Org-mode is composed of the following articles:

  1. Configuring Emacs for Org-mode
  2. Project folder structure
  3. Anatomy of a Org-mode file
  4. Tangling all project files (this post)
  5. Publishing documentation in multiple formats
  6. Unit Testing

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Literate [Clojure] Programming Using Org-mode

Literate Programming is a great way to write computer software, particularly in fields like data science where data processing workflows are complex and often need much background information. I started to write about Literate Programming a few months ago, and now it is the time to formalize how I create Literate Programming applications.

This blog post belong to a series of posts about Literate [Clojure] Programming:

  1. Configuring Emacs for Org-mode
  2. Project folder structure (this post)
  3. Anatomy of a Org-mode file
  4. Tangling all project files
  5. Publishing documentation in multiple formats
  6. Unit Testing

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Optimal Emacs Settings for Org-mode for Literate Programming

For some time I have been interested in using Emacs and Org-mode for developing Clojure in a Literate Programming way. I discussed the basic ideas, some of the benefits of doing so, etc, etc. It is now time to start showing how I am doing this, what are the rules of thumb I created, what is the structure of my programs, etc.

However, before I start writing about any of this, I think the next step is to explain how I configured Org-mode to have a frictionless experience to develop my applications in Literate Programming using Org-mode. Then in a subsequent series of blog posts I will explain how I structured my Clojure project, what is my development workflow, etc.

Note that if you don’t have Emacs setup for Clojure/Cider, I would encourage you to read this other blog post which explains how to setup a Clojure environment in Emacs.

This is the first post of a series of blog posts that will cover the full workflow. I will demonstrate how I do Literate Programming for developing a Clojure application, but exactly the same workflow would work for any other programming language supported by Org-mode (Python, R, etc.). The only thing that is required is to adapt the principles to the project structures in these other languages. The series of blog posts will cover:

  1. Configuring Emacs for Org-mode (this post)
  2. Project folder structure
  3. Anatomy of a Org-mode file
  4. Tangling all project files
  5. Publishing documentation in multiple formats
  6. Unit Testing

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Improving org-babel-clojure

In a previous blog post, I started to play with org-babel-clojure to improve its capabilities such that Clojure gets better integrated into Org-mode for creating notebooks and Literate programs. The first thing I wanted to do is to remove the 20 seconds timeout that was defaulted with the nrepl. That meant that it was not possible to run procedures for longer than 20 seconds before it died with a timeout. Once this was implemented, the next step was to add a new feature to see the underlying process of a code block. Because the nature of my work (extensive work with big datasets), my procedures take time to run (minutes… hours…) and much information [about the process] is output to the terminal. However, in the org-babel-clojure implementation, you had to wait until the code was executed before being able to see the processing. What I did at the time is to add a new :async code block parameter which told org-babel-clojure to output all the output of the nrepl, when it was being processed, in a new window.

That worked like a charm. However, after much interaction with Nicolas Goaziou, one of the core maintainers of Org-mode, it was clear that my implementation was not an asynchronous implementation but really just a live processing output.

At the same time, I did find another major irritant: if an exception was raised in my Clojure code, then nothing was output to Org-mode, it was simply silently dying. The only way to see the exception was to switch to the Clojure major mode (using C-c ') and to rerun the code block.

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