Fix genetic_relatedness to allow single sample set with self-comparisons

[andrewkern]

Description

This PR fixes issue #3055 where genetic_relatedness would fail when computing self-comparisons with a single sample set. As @petrelharp pointed out there is no reason this shouldn't be allowed for certain statistics, including genetic_relatedness

The Problem

Previously, calling genetic_relatedness with a single sample set and indexes referring to that set would raise an error:

ts.genetic_relatedness([[0]], indexes=[(0,0)])
# TSK_ERR_INSUFFICIENT_SAMPLE_SETS: Insufficient sample sets provided

This occurred because the underlying C API validates that at least k=2 sample sets are provided for k-way statistics, even when the indexes only reference a subset of those sets.

This PR

The fix adds an allow_self_comparisons parameter to the internal __k_way_sample_set_stat method, which is only set to True for genetic_relatedness. When enabled:

1. The method validates that all indexes reference valid sample sets
2. If fewer than k sample sets are provided, it pads the list with dummy sample sets to satisfy the C API requirement
3. The dummy sets are never accessed during computation since only the sets referenced by the indexes are used

This ensures that:

• Only genetic_relatedness behavior is changed
• Other statistics (like Fst) continue to enforce the minimum sample set requirement
• The C API contract is satisfied without modifying the C code

Further, this PR sets the stage for allowing for other appropriate k-way stats to be computed with self comparisons by setting a flag.

Testing

Added comprehensive tests for all three computation modes (site, branch, node) to verify:

• Single sample set with self-comparison works correctly
• Multiple samples within a single set work correctly
• The fix doesn't affect other statistics

All existing tests continue to pass, but @petrelharp this would benefit from you specifically looking over what I've done to be sure you're okay with the way I've implemented allow_self_comparisons

Fixes #3055

PR Checklist:

• Tests that fully cover new/changed functionality.
• Documentation including tutorial content if appropriate.
• [] Changelogs, if there are API changes.

I'm not sure if I should touch the changelogs here?

[codecov]

Codecov Report

Attention: Patch coverage is 91.66667% with 1 line in your changes missing coverage. Please review.

Project coverage is 89.61%. Comparing base (3c0a99a) to head (cd830f7).

Files with missing lines	Patch %	Lines
python/tskit/trees.py	91.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3235   +/-   ##
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  Coverage   89.61%   89.61%           
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  Files          28       28           
  Lines       31983    31995   +12     
  Branches     5888     5892    +4     
=======================================
+ Hits        28660    28671   +11     
  Misses       1888     1888           
- Partials     1435     1436    +1     

Flag	Coverage Δ
c-tests	86.59% <ø> (ø)
lwt-tests	80.38% <ø> (ø)
python-c-tests	88.15% <ø> (ø)
python-tests	98.79% <91.66%> (-0.02%)	⬇️
python-tests-numpy1	52.35% <0.00%> (-0.09%)	⬇️

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Files with missing lines	Coverage Δ
python/tskit/trees.py	98.82% <91.66%> (-0.04%)	⬇️

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[jeromekelleher]

I think we'll need to wait for @petrelharp to get informed review on this one.