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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/compare_all_dist.py
+2 -2
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@@ -1,9 +1,9 @@
#!/usr/bin/env python3
"""Compare all reference distance matrices against obikmer distance outputs.
"""Compare all reference distance matrices against obikmer phylo outputs.
Reads from:
reference_dist/ — ground-truth matrices computed by build_reference_dist.py
obikmer_dist/ — matrices produced by `obikmer distance`
obikmer_dist/ — matrices produced by `obikmer phylo`
Handles label reordering: both matrices are sorted by genome label before
element-wise comparison, so column/row order differences are irrelevant.