Restructure the project by moving the standalone compare_sparse utility into an example directory, removing Sankoff parameter configurations and benchmark scripts, updating version control ignores, and expanding the test suite with diagnostic checks and performance benchmarks.
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.
Introduces a new predicate module in obikindex that implements genome metadata predicate parsing, evaluation, and group classification using three-valued logic. Extends the IndexMeta API with methods for single-predicate filtering and group quorum filtering. Updates obikmer command modules to delegate filter construction and matching to the centralized index API, removing local definitions and simplifying call sites.
Re-enables the `numa` feature in CI workflows to prevent container/cgroup deadlocks while preserving validation correctness. Fixes concurrent test race conditions by replacing thread-local parameter storage with process-wide atomics and mutex locks. Integrates `tracing-subscriber` for structured logging and adds thread-ID tracking to debug worker lifecycles. Additionally bumps the crate version, updates `.gitignore`, documents experimental evolutionary distance pipelines, and refactors hardcoded test constants.
Add the `obipipeline` crate and replace sequential scatter/gather logic with a concurrent pipeline using `Flat` and `Transform` stages. Introduce `SiblingAnnexStats` API to compute distributions, and add CLI flags to `distance.rs` for constructing the annex and exporting statistics as CSV.
Introduce the siblingannex module in obicompactvec to store per-slot minorant flags and sibling counts in a memory-mapped annex file. Add a scatter-gather pipeline in obikindex to compute these values across index layers and write them to .psib files. Implement central_canonical_neighbors in obikseq for generating strand-aware k-mer variants around the middle base. Expose rolling statistics in obiskbuilder and update dependency graphs accordingly.
Refactor the Gitea release pipeline to generate releases via API and upload binaries using a shared ID. Automate changelog generation by fetching recent commits with `jj log` and producing markdown notes via `aichat`. Convert `hwlocality` to an optional dependency gated by a default `numa` feature, providing fallback implementations for graceful degradation when NUMA support is disabled. Bump obikmer to 1.1.18.
Replaces the global Rayon pool with per-NUMA-node thread pools that pin worker threads to their respective nodes, leveraging Linux first-touch allocation to reduce cross-NUMA memory contention and improve cache locality. Integrates the `hwlocality` crate with a vendored build, includes graceful fallbacks for single-socket or non-Linux systems, and updates dependency constraints. Also adds installation and architecture documentation, and corrects parallelism detection in the partitioner.
Introduce CpuSample to measure process-level CPU efficiency and wall-clock time. Use crossbeam-channel to distribute partition merging tasks to a dynamic worker pool that scales based on CPU utilization, capped at half the available cores. Update diagnostics to track pool usage.
This change adds the `obikseq` crate as a local dependency and inserts `set_k` and `set_m` calls across index creation and command modules. By synchronizing the runtime's global k-mer and minimizer dimensions with the loaded index parameters, downstream sequence processing and partitioning operations now consistently use the correct structural constraints.
This commit introduces a new `distance` CLI subcommand that computes pairwise genomic distance matrices using configurable metrics (Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger). It optionally generates phylogenetic trees (NJ or UPGMA) in Newick format and outputs results as CSV. The implementation adds a robust distance computation backend that dynamically routes to optimized backends based on index configuration, supports parallel iteration, and gracefully handles missing data. Additionally, it adds a `dump` task for exporting k-mer to genome mappings as CSV, introduces an `InvalidInput` error variant, updates dependencies to support numerical operations and tree construction, and performs minor module reorganizations.
Refactors obikindex and obikpartitionner to delegate index construction to a new layered MPHF implementation. Adds resume-safe building with abundance filtering and count persistence, while introducing a PartitionMeta struct for JSON configuration persistence. Updates OKIError to wrap layer-specific errors, replaces single-path extraction with full path collection and logging, and registers new internal dependencies across the workspace.
Extracted core indexing logic, state tracking, and metadata management into a new `obikindex` crate. Refactored the `index` and `unitig` commands to leverage the `KmerIndex` abstraction and state-driven pipeline transitions. Removed obsolete CLI subcommands (`count`, `fasta`, `longtig`, `partition`) and their associated pipeline steps. Updated FASTA writing utilities for single-line output and deterministic identifiers, and refreshed workspace dependencies.
Eric Coissac