6 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	26026288de	refactor(benchmark): consolidate generated artifacts under run/ directory ... Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.	2026-08-29 00:20:31 +02:00
Eric Coissac	54e4600120	feat: add batched int group stats API and expand benchmark variants ... Introduces a `batch_int_group_stats` API for computing presence counts, sums, minimums, and maximums across sparse and dense matrix representations. The selection layer now utilizes this batched approach to optimize aggregation semantics for boolean and numeric operations. Additionally, reorganizes the benchmarking infrastructure to support querying across presence and count index variants in both dense and sparse formats, including new packing scripts and updated statistics aggregation.	2026-08-28 23:37:16 +02:00
Eric Coissac	89ea077456	Add benchmark pipeline for dense and sparse query testing ... Introduces a complete query benchmark track to evaluate performance and verify consistency between dense and sparse index formats. Adds scripts to simulate fixed-size paired-end reads, pack a sparse presence index, execute queries in both modes, and capture wall time and RSS metrics. Includes a verification step that compares outputs by read ID to ensure content identity across parallel processing. Updates build configuration, documentation, and ignore patterns to support the new pipeline for two microbial specimens.	2026-08-20 13:59:12 +02:00
Eric Coissac	dd889854cb	rename distance subcommand to phylo ... Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.	2026-08-15 10:07:03 +02:00
Eric Coissac	469e53b6f5	Add genomic distance benchmarking suite and test data ... Introduces scripts to compute and validate pairwise genomic distance matrices across multiple metrics. Updates the Makefile with build and comparison targets, adds .gitignore rules for generated outputs, and includes test CSV matrices and a Newick phylogenetic tree for validating the distance computation pipeline.	2026-06-22 18:24:30 +02:00
Eric Coissac	c694e1f2b0	feat: add benchmark pipeline, expose APIs, and enforce strict paths ... Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.	2026-06-22 10:18:33 +02:00