3 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	52f26809af	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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.	2026-08-29 00:19:31 +02:00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