7 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	b5ec0122d0	Rename obikpartition crate to obikpartitionner ... Update all dependent crates and internal imports to reference the renamed module. Expose configuration parameters and genome metadata through new public accessor methods in the index API, and update documentation comments to align with the new package name.	2026-08-20 19:43:00 +02:00
Eric Coissac	9379bbaad8	refactor: rename obikpartitionner crate to obikpartition ... Update Cargo manifests, dependency paths, and Rust imports across the workspace to reflect the `obikpartitionner` to `obikpartition` rename. Synchronize architecture and implementation documentation with the new module structure. Fix minor syntax issues in test assertions to ensure compilation compatibility. No behavioral or API changes are introduced.	2026-08-20 16:41:22 +02:00
Eric Coissac	5a9d903e51	chore: update dependencies and adapt to updated crate APIs ... Bumps core dependencies including ndarray, rand, hashbrown, niffler, ureq, sysinfo, indicatif, lru, and remove_dir_all. Adapts source code to accommodate breaking changes by migrating RNG initialization, adjusting HTTP response handling, and replacing the fs4 crate with standard library file locking. Adds a planning document for query benchmarking and sparse index regression tests.	2026-08-20 13:45:41 +02:00
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