When comparing Docco vs JSDoc, the Slant community recommends JSDoc for most people. In the question“What are the best JavaScript documentation tools?” JSDoc is ranked 1st while Docco is ranked 2nd. The most important reason people chose JSDoc is:
The community behind JSDoc has built sever templates and other related tools that allow you to use JSDoc in a simpler and more efficient way.
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Pros
Pro Great for beginners
Since Docco doesn't enforce any comment style or rules, it's great for beginners who can instantly pick up without having to learn any new syntax or style.
Pro Markdown support
All the comments are run through a markdown parser, while all the code is run through Highlight.js for code highlighting.
Pro Numerous templates available
The community behind JSDoc has built sever templates and other related tools that allow you to use JSDoc in a simpler and more efficient way.
Pro Grunt plugin available
For people who like to use Grunt, there's a Grunt plugin available.
Cons
Con Does not enforce a pattern in writing comments
Since Docco only accepts comment lines starting with double slashes, it does not really enforce any pattern in writing comments, at least not as much as it would if it would use comment blocks. This can bring a huge disparity and even make it harder for Docco to generate good documentation as the project grows larger.
Con Only provides an output of the API
JSDoc only provides a linear output of the API and not really a visually appealing or any information other than the methods and what they do. It's very technical so it may be hard for beginners to read documentation generated by it and understand it.
