Without documentation, software is just a black box. And black boxes aren’t anywhere near as useful as they could be because their inner workings are hidden from those who need them in the open.

Software documentation turns your software into a glass box by explaining to users and developers how it operates or is used.

You’ve probably seen documentation before, but if you need a refresher, here’s an example from Slack‘s API:

Slack API Documentation-d

As you can see, Slack explains everything about its API in excruciating detail. Any related pages are linked, there’s a sidebar with easy-to-access topics, and screenshots of what the user can expect to see.

Documentation can be as simple as a README.MD file in the repository, and it can be as complex as an entire subdomain with a custom design like Slack’s API docs (above). Whatever you choose, there are several tools to use to make the process easier.

Key Highlights: Understanding Software Documentation Tools

  1. Documentation Importance: Converts software from a “black box” to a “glass box,” clarifying operations for users and developers.
  2. Markdown Editors: MarkdownPad, iA Writer, and SimpleMDE are favored for writing software documentation, offering simplicity and compatibility with version control.
  3. Non-Markdown Solutions: For those preferring alternatives, reStructuredText editors and specific plugins for vim, Emacs, and Eclipse offer flexibility in documentation creation.
  4. Hosting Solutions: Read The Docs and GitHub (& GitHub Pages) stand out for their ability to host and manage documentation efficiently, supporting version control integration.
  5. Internal Documentation: Dropbox Paper and Process Street are excellent for creating and maintaining internal documentation, offering collaboration and process integration features.
  6. API Documentation: Tools like Atlassian REST API Browser and Apiary specialize in API documentation, facilitating discovery and interaction with APIs.
  7. Automatic Generation: For large codebases, tools like Doxygen, GhostDoc, Javadoc, and Docurium can automatically generate documentation, saving time and ensuring consistency.
  8. Choosing the Right Tools: Selection depends on the documentation’s complexity, the team’s familiarity with programming languages, and the need for internal vs. external accessibility.
  9. Final Consideration: While tools can simplify the documentation process, the quality of content and its accessibility to the intended audience are paramount for effective software documentation.

Top Writing Tools for Software Documentation

Software documentation is often written in markdown to allow for hyperlinks and formatting while keeping it plain text so it can live alongside the code files in version control.

That means that a lot of my choices for writing tools are simple markdown editors that make the writing experience enjoyable. Additionally, there are also a couple of very effective non-markdown solutions thrown in there.

MarkdownPad (Windows)

With a free and premium version — both with a ton of great features — MarkdownPad is the most popular markdown editor for Windows. It’s optimized for blog posts, websites, articles, READMEs, and, of course, software documentation.


You can get MarkdownPad for free, or get the premium version for $14.95.

iA Writer (Mac)

iA Writer is a simple, beautiful markdown editor with a library feature meaning you can easily reference back other documents in the sidebar. It’s missing internal links between documents like you’d expect there to be in software docs, but you can always do a pass on those when it’s in its final form (that is, if it’s going to end up on the internet in a site).

If you write your whole documentation in one, broken-up page, you can use page jump anchors to help users navigate.

iA Writer costs $9.99 from the Mac App Store.

SimpleMDE (browser)

While you can technically write markdown in any text editor because it is a way to format plain text, not strictly a ‘tool’, it won’t surprise you that it’s also possible in your browser! SimpleMDE is a both a functional markdown editor built on JavaScript and an open source project to learn from and adapt for your own use, if necessary.


SimpleMDE is 100% free! Get the source on GitHub here.

reStructuredText editors

Markdown is one of the two most commonly used languages for writing software documentation, but there’s another we’ve not looked at so far, and that’s reStructuredText. It’s very similar to markdown, but worth learning for software documentation purposes.

Docutils, the creator of reStructuredText, has put together a list of reStructuredText editors here, which includes:

  • A plugin for vim
  • Emacs (in rst mode)
  • A plugin for Eclipse
  • A plugin for TextWrangler/BBEdit
  • NoTex (for browsers)

The point of reStructuredText is that it’s easy to convert between different formats, especially from plain text to a static website. See more info here.

Software Documentation Hosting Options

It’s no good having just a bunch of text files living on your computer.

They need to be accessible by developers and users, which you’re most likely going to do by hosting the docs on the internet since it isn’t the 1980s.

Read The Docs

It’s remarkable that Read The Docs is free when you see all that it can do. Similar to GitHub, you can create as much open source material as you like that gets openly indexed on the site, but it’s going to cost you if you want to make the docs private and internal to your company. For our purposes, it’s likely you’re going to be alright with having the docs readily available for users on the web.

Read The Docs-d

The reason Read The Docs is so good is that you can effortlessly import documentation from any version control system including Git, Mercurial, Subversion, and Bazaar. It also supports webhooks so the docs get built automatically whenever you commit code.

Check their Getting Started guide to get a feel for how it works and how your docs would behave when hosted there.

GitHub (& GitHub Pages)

If you’re using GitHub to manage version control for your software, you have, at the bare minimum, a README.MD file in the repository. To use GitHub for documenting your software, like millions of others have done in the past, just fill that README in with markdown.

A great example is sferik’s t repository, screenshotted here:

GitHub Software Documentation for t

If you want more than just one sheet of formatted text, you can take advantage of GitHub’s Pages tool (you get one free webpage + hosting with each GitHub account, and you can even route a custom domain to it).

Pages even has great looking default themes that make your documentation look professional.

Electron Software Documentation-d

Above is atom.io documentation for Electron hosted on GitHub. It’s a smart choice because it automatically works with GitHub’s version control, just like the rest of your software.

Dropbox Paper (for internal use)

For internal software documentation use, Dropbox Paper is an excellent choice. Like its predecessor Hackpad, you can use it to create a private wiki for employees. You can link documents together, insert code blocks, images and page jumps, just as you’d demand from any documentation tool.

Dropbox Paper Software Documentation

As you can see from the comments on the right, you can also use it to go through approval processes and collaborate over the creation of documentation.

Overall, it’s a great tool for internally developing and creating documentation, perhaps with the view to publicize it later, or just keep it for internal use.

Process Street (for internal use)

For training new developers and keeping your documentation living all in the same place, Process Street is a solid choice for software documentation. We use our own product for as much as possible, and since it’s a way to create and share structured documents, it lends itself perfectly to this purpose. Check it out:


It supports headings, text, video, image, and code blocks (to name a few), so if it can be documented it can be documented in Process Street.

Atlassian REST API Browser (for API use)

Atlassian’s REST API Browser (RAB) is included in JIRA Server, Confluence Server and Stash instances by default. It’s built for discovering APIs available for use in JIRA/Confluence environments, and also a place to host your documentation. If, of course, your API fits the bill.

RAB Software Documentation

Document your API using this tool to give your JIRA/Confluence compatible API more exposure. Check here for Atlassian’s documentation on doing that.

Apiary (for API use)

As well as being a place where bees live, Apiary is a dedicated host for API documentation. Write in markdown, add mock API calls and Apiary collates that into something like you see below:

apiary software documentation

Anyone can test the API without having to go into the app or actually program a call, which makes it a super accessible way to share your API, document it in-depth, and boast about what it can do.

Apiary 2-d

Best Tools to Automatically Generate Documentation from Source Code

There’s nothing like the human touch when it comes to documentation (it’s clear in the docs of Slack and Giphy, to name a couple).

However, as a starting point (especially for huge source libraries), it’s best to generate the skeletal documentation automatically.

This work by analyzing the source’s functions and comments, and there are a few different options depending on language:

  • Doxygen (C, C++, C♯, D, Fortran, IDL, Java, Objective-C, Perl, PHP, Python, Tcl, and VHDL)
  • GhostDoc (C#, Visual Basic, C++/CLI, JavaScript)
  • Javadoc (Java only)
  • Docurium (Ruby)

Before you go ahead and rely solely on automatic generation, I’d suggest reading this StackExchange thread which weighs the pros and cons.

Final Words on Software Documentation Tools

There are plenty of fancy solutions, quick fixes and tools that are (quite honestly) almost identical.

What matters in the end is that you’re going to have to write comprehensive documentation and host it somewhere the user can get to it. Other than that, you’re free to use whatever makes your life easier.

I hope you find your new favorite tool in this list.