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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

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ObiTax Lua Module Documentation

This Go package (obilua) provides Lua bindings for the obitax taxonomy management module of OBItools4, enabling scripting in Lua with rich taxonomic operations.

Core Features

Type Registration: Registers two main types in the Lua state: Taxonomy and Taxon.
Factory Functions:
- obitax.Taxonomy.new(name, code [, charset]): Creates a new taxonomy instance.
- obitax.Taxonomy.default(): Returns the globally configured default taxonomy (raises error if none exists).
- obitax.Taxonomy.has_default(): Boolean check for existence of a default taxonomy.
- obitax.Taxonomy.nil: Represents the nil taxon (used for missing data).

Taxonomy Object Methods

name(): Returns the taxonomy name (e.g., "NCBI").
code(): Returns the internal code used for taxonomic identifiers (e.g., "txid").
taxon(id): Retrieves a taxonomic node by ID; returns:
- the corresponding Taxon object,
- raises an error if not found or on alias resolution when FailOnTaxonomy() is enabled.

Taxon Object Support

A dedicated registerTaxonType (not shown here) exposes a Lua-accessible Taxon type with methods like rank, parent, and string representation.

Integration

Built on top of standard OBItools4 types (obitax.Taxonomy, obiutils.AsciiSetFromString).
Leverages GopherLua for seamless interoperability between Go and Lua.

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