4 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	8bb1d52514	disable default features for obisys dependency ... Update obisys dependency configuration across multiple crates to explicitly set default-features = false. This restricts compilation to only explicitly enabled feature flags, affecting build resolution and potentially compile-time paths or binary size. Also updates the obikmer package version to 1.3.1.	2026-08-29 08:13:49 +02:00
Eric Coissac	00ba968628	Introduce obikalgorithm crate to unify pipeline algorithms ... Define a shared Algorithm trait with an associated Output type and a parameterless run(&mut self) method. Refactor PartitionRouter, Dereplicator, Counter, and LayerBuilder to implement the trait, standardizing receivers to &mut self and moving configuration and progress callbacks to dedicated builder setters. Decouple error handling using a generic boxed error type and update workspace dependencies accordingly.	2026-08-21 22:03:08 +02:00
Eric Coissac	da3aa5a2cb	refactor: extract index construction state tracking into extension trait ... Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.	2026-08-21 10:38:51 +02:00
Eric Coissac	96b6517541	refactor: rename obikindex to obikindexer	2026-08-21 05:29:34 +02:00