API Reference

Python API for the skimindex package. All public modules are documented below.

Module	Description
config	TOML configuration loading, path resolution, singleton access
config.validate	Config validation — structural checks and cross-section dependencies
datasets	Dataset abstraction — resolves config datasets to Data objects
sources	Source and artifact path helpers, resolve_artifact()
processing	Processing type registry, pipeline builder, Data abstraction
stamp	Stamp file management — tracks completed pipeline steps
sequences	Sequence file discovery utilities
naming	Canonical species/taxon name helpers, genome path parsing
log	Logging — levels, colors, file output
unix	Unix CLI tool wrappers (plumbum-based): pigz, ntCard, datasets, OBITools4, SRA Toolkit