4 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	fceb523f1a	chore: disable default features for obikindex ... Explicitly sets `default-features = false` for the `obikindex` dependency to ensure no default features are activated during dependency resolution and compilation.	2026-08-17 12:33:59 +02:00
Eric Coissac	45b19503a1	Add proportional subsampling and Shannon entropy calculation ... Introduces `--subsample N` and `--shannon` CLI flags to cap retained variable families via proportional reservoir sampling and compute per-family Shannon entropy. Updates the family scanning API to support explicit selection filtering with early-exit optimization, resolving an indexing drift issue in monomorphic layers. Streams entropy metrics for 15-state and 4-nucleotide spaces directly to CSV while maintaining parallel processing across sibling layers.	2026-08-16 21:31:06 +02:00
Eric Coissac	fecfe84ea6	Move sibling annex implementation to obikphylo siblings module ... Relocates `SiblingAnnex`, `FamilyMask`, and `SiblingAnnexBuilder` from `obicompactvec` to the local `obikphylo::siblings` module. Replaces the previous implementation with a memory-mapped version using `memmap2`, featuring a 2-byte-per-slot layout, explicit bitfield manipulation, and support for concurrent atomic writes. Updates all sibling module imports to local paths and adds the `memmap2` dependency to `obikphylo`.	2026-08-16 21:04:14 +02:00
Eric Coissac	5997de6707	Extract phylogenetic sibling logic into new obikphylo crate ... Relocate the `siblings` and `cardcomp` modules from `obikindex` to a dedicated `obikphylo` workspace member. Convert inherent methods on `KmerIndex` into extension traits, update import paths across `obikmer`, and add supporting accessor methods to `obikseq` and `obilayeredmap`. This restructuring reduces the public API surface of `obikindex` while organizing phylogenetic iteration, caching, and distance calculation logic under a dedicated crate.	2026-08-16 14:30:34 +02:00