Summary

• Three independently callable subcommands: disjoint-group, per-group partition, assemble-groups
• YAML manifest as handoff between steps
• Works for paired (multi-locus) and unpaired (single-locus) data
• Works for simulated and real data
• Disjoint grouping does not degrade clustering accuracy (validated HA and vsearch against standard partition)
• CDR3 length disjointness validated on simulated and real data
• Test framework integrated into test/test.py with reference results for all four configs
• No regressions (partis-test.py --quick and --paired --no-simu pass)

Test plan

• partis-test.py --quick passes
• partis-test.py --paired --no-simu passes
• Disjoint grouping tests pass for paired simu, paired data, unpaired simu, unpaired data
• Clustering accuracy comparison shows no degradation

Related: #337