Documentation in Practice

Last updated on 2026-06-22 | Edit this page

Overview

Questions

What does developer documentation look like in practice?
What does user documentation look like in practice?
What belongs in a README, a docstring, and a citation file?

Objectives

Become familiar with real-life examples of documentation.
Practice writing different kinds of documentation.
Understand the role of the README, docstrings, and citation/licensing files.

Start the Right Way: the README

Before any framework or tool, almost every project’s documentation begins with a single file: the README. It’s the first thing a visitor sees on GitHub, and for many research projects it’s the only documentation that exists. A good README answers a newcomer’s questions fast:

Section	Answers
What and why	What does this do, and why would I use it?
Install	How do I get it running?
Usage / quick example	Show me the simplest thing that works.
License	Can I use it, and how?
How to cite	How do I give credit in a paper?
Contributing / contact	How do I report a bug or get help?

You don’t need all of these on day one — but a README that covers what/why and a quick example already puts you ahead of most research code.

Document the Why, Not the What: Docstrings and Comments

Two kinds of in-code documentation do most of the day-to-day work:

Docstrings describe what a function/class does and how to use it — its inputs, outputs, and behavior. They’re written for the person calling your code (and power tools like Sphinx, covered next episode).
Inline comments explain why a particular piece of code is the way it is — the non-obvious decision, the workaround, the edge case.

The better practice: comment the why, not the what. Code already says what it does; a comment like # add 1 to i is noise. A comment explaining why you add 1 (an off-by-one in an upstream API, say) is gold.

Developer Documentation Examples

Documentation Type	Explanation	Example
Team processes	This type of documentation documents the expected development processes within a team. These generally include an objective, stakeholders, and steps to follow.	US-RSE’23 Website Repository `CONTRIBUTING` guide
Styles and standards	This type of documentation states the expectations on styles and standards within a code. This can include preferred tools, usage of existing style guides, and project or domain-specific standards.	Pyomo’s Required Coding Standards
API	This type of documentation is both developer and user documentation. From a developer perspective, this documentation elaborates the intent of the code, e.g., what the code is supposed to be doing, which can improve maintainability.	Spack’s API Documentation

Discussion

PRACTICE: Euler’s Method Documentation

Have you heard of Euler’s Method? It’s a way to calculate a numerical approximation for the value of a function, based on a starting value x_0, a particular step size h, and the derivative of the function.

Write some documentation for the following code snippet:

PYTHON

class EulersMethod:
    def deriv(self, x, y):
        return y**2 + y*x + x**3
    def approx(self, y, x, h):
        y_j = y + h*self.deriv(x, y)
        x_j = x + h
        return y_j, x_j

Bonus: How would you improve this code to make it more clear?

GenAI Bonus: Ask an LLM to write a docstring for this class. Then critique its output: Did it correctly describe what deriv and approx actually do? Did it invent behavior the code doesn’t have? Did it explain the why? Fix what it got wrong. This is the review skill that matters most when documenting with AI.

User Documentation Examples

Documentation Type	Explanation	Example
Installation	This documentation is meant to help users get a package installed and working properly. Frequently, it will detail not only the different methods of installing the software, but also simple explanations of how to ensure it was installed correctly (e.g., a sanity test).	NumPy Installation Instructions
Debugging and troubleshooting	This type of documentation helps users troubleshoot common errors. This is normally built from previous questions or common mistakes, such as invalid setup, options, or inputs.	Pyomo Common Warnings and Errors
Tutorials and examples	This type of documentation is meant to show users, step-by-step, on either small or real-world scales, how a software package is supposed to be used. This documentation helps with clarifying the developers’ intended use and acts as a starting point for users.	Pandas Getting Started Tutorials

Discussion

PRACTICE: Install Python

Assume that you have a new team member who does not have Python on their machine and wants to install it. They send you an email to ask how they should do it.

Do you have all the information you need to answer this question? Why or why not?
Given only the email, write instructions detailing how to install Python from python.org.

Callout

REMINDER: Culture, Context, Experience

Keep in mind culture, context, and experience when writing your instructions.

Callout

Make It Citable: CITATION and LICENSE

Two small files matter a lot for research software:

CITATION.cff is a simple, structured (Citation File Format) file telling people how to cite your software. GitHub reads it and shows a “Cite this repository” button automatically — so your work gets credited correctly in papers.

These pair naturally with the contributing guides and pull-request workflow from the previous session. (INTERSECT’s own lesson repos include both.)

Key Points

There are numerous examples of different types of documentation in practice, each with its own intended purpose.
A project must pick the documentation that makes the most sense for its use case and domain.
The README is the front door; docstrings document the why; LICENSE and CITATION.cff make research software reusable and citable.
GenAI can draft documentation quickly, but you must review it for accuracy.