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Following Max's advice I thought I just create issue for every open questions, so that is is easier to track things.
Bruno: I'm a fan of having literate code and using docco. I think it's a good practice to write the comments as docs when you're writing the code, and that way you don't have to figure out where the documentation is.
However, this isn't of course an alternative to a global API doc. As I mentioned, some projects do global APIs manually, like underscore, express, nodejs and socket.io. However, something automatic would be better. I'm currently exploring doxx as it seems to be able to generate a single doc for multiple modules. If doxx can solve most of the problem, we can then tweak it to generate an output with some of Biogems features.
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We are very happy that we are building an open registry for bio npm packages.
For documentation we agreed for the moment that the Readme.md is the simplest common denominator. On our registry you will just get an extra badge for an existing ReadMe and also for external documentation like jsdoc.
However what we want to achieve are visually appealing snippets for components.
For more info (draft!) how a visulization component could specify those specs have a look here:
Sounds good, displaying the README.md in the registry is what NPM is also doing and seems to be the simplest solution. As for combining all the docs into a global API, I'm just concatenating the docco html (with some tweaks) for doc.bionode.io, but this could be improved.
I'm closing this as the documentation in the BioJS registry issue seems solved. As for global documentation, we can continue at #27