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rename distance subcommand to phylo

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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.
This commit is contained in:
Eric Coissac
2026-08-15 10:07:03 +02:00
parent 79346c0c86
commit dd889854cb
19 changed files with 49 additions and 46 deletions
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benchmark/build_reference_dist.py
+2 -2
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@@ -2,10 +2,10 @@
"""Compute reference pairwise distance matrices from per-specimen .npz kmer indexes.
Reads all .npz files in reference_index/ (each containing sorted uint64 `kmers`
and uint32 `counts`), computes all distance metrics supported by `obikmer distance`,
and uint32 `counts`), computes all distance metrics supported by `obikmer phylo`,
and writes one CSV per metric to reference_dist/.
Output CSV format matches `obikmer distance --output`:
Output CSV format matches `obikmer phylo --output`:
- first row: "genome", then specimen names
- subsequent rows: specimen name, then float or int values