GAIn Development

This section is the in-depth description of GAIn as a Python library: the objects you touch when you embed GAIn in your own code, add a resource implementation, or write an annotator plugin. It is written for the extender — someone building on GAIn — rather than for GAIn’s own contributors.

If you have not used the Python interface before, start with GAIn Python interface; that page is the getting-started guide, and the split between it and this section is depth, not audience. And if what you are writing is pipeline YAML or a command line rather than Python, you want the user pages instead — Genomic resources and repositories for resources and repositories, Annotation infrastructure for pipelines and annotators. Everything on this side of that line is Python.

The chapters build bottom-up, substrate before the things that consume it:

1. Working with resources in Python — the resource half of the declared API: repositories and resources, reference genomes, gene models, the three kinds of score, histograms, and the seam for adding a resource type.

2. Annotators — planned (#1144).

3. Complete module index — the complete generated API tree, for when you already know the name you are looking for.

Attention

Draft marker D1 — the one unwritten chapter. The numbered list above names chapter 2 so the reader sees the shape of the guide, but the toctree below deliberately leaves it out: a toctree entry for a page that does not exist is a build warning, and a placeholder page that says “coming soon” would go live on the site the moment this merges. Decide which of the three you want here — (a) list-but-don’t-link as now, (b) a stub page that ships a one-paragraph placeholder, or (c) drop the line from the list until #1144 lands. Option (a) is the draft’s choice because it publishes nothing that later has to be unpublished.

• Working with resources in Python
  • Where the line falls
  • The shape of the API
  • Not covered here
• Complete module index
  • gain package