7 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	6b0c0867cc	implement hybrid hard-link copy strategy for directory bootstrap ... Introduces recursive directory replication functions that default to hard-linking for space efficiency, with automatic fallback to full file copying on cross-filesystem failures. Enforces mandatory real copies for presence and counts subdirectories to guarantee independent data matrices before merging, while preserving the existing separation between immutable index files and mutable matrix files.	2026-08-28 23:18:34 +02:00
Eric Coissac	4b6005962e	Rename PersistentCompactIntMatrix to PersistentIntMatrix ... Update all matrix type references, imports, and instantiations across the codebase to use the new PersistentIntMatrix name. The change also includes standardizing code formatting, such as multi-line statements and import ordering, without altering any behavioral logic or public API contracts.	2026-08-28 19:59:59 +02:00
Eric Coissac	354e6f9bf1	Add unified matrix builder abstraction and k-mer filtering CLI ... Introduces a unified MatrixBuilder abstraction for persistent bit and integer matrices, replacing custom dispatch enums and boolean flags across consumers. Refactors index, merge, and select layers to adopt explicit merge modes and centralized lifecycle management. Adds a complete k-mer filtering implementation with partition-level processing, progress tracking, and a new CLI subcommand supporting configurable predicates and thresholds.	2026-08-26 14:19:15 +02:00
Eric Coissac	cbf6893f38	Add configurable sparsity flag to index finalization and merge CLI ... Extends `KmerIndex::finalize_indexed` to accept a `sparse` boolean parameter, enabling control over whether output presence matrices are packed in a compact sparse format or stored densely. The merge command now exposes a `--dense` flag to invert this setting, defaulting to the existing sparse representation. Call sites in select and rebuild modules pass `false` to preserve current behavior. A benchmark lock file is also added for dependency tracking.	2026-08-22 17:36:50 +02:00
Eric Coissac	5048f43eea	Start of a huge refactoring	2026-08-22 17:03:53 +02:00
Eric Coissac	fc4464a0ef	Extract index modules into specialized workspace subcrates ... This commit partitions the obikindex crate into multiple focused subcrates (obikfilter, obikmerge, obikquery, obikrebuild, obikselect, obikstats, obikdump, and obikidxcache) to reduce coupling and clarify module boundaries. It standardizes error handling across the workspace using OKIError and OKIResult, updates index APIs to support lazy, disk-backed partition access, and migrates NUMA system utilities to a new obisys crate. All modifications are structural, focusing on dependency graph expansion, import path updates, and API surface reorganization without altering core runtime behavior.	2026-08-22 06:25:28 +02:00