Modernize C++ in NNI distance

[ms609]

Address valgrind concerns

[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
ClusteringInfoDistance(tr200)	⚪ NSD	0.35%	681 → 683, 675
ClusteringInfoDistance(tr50)	⚪ NSD	-0.13%	395 → 399, 392
LAPJV(test2000)	⚪ NSD	1.41%	90.9 → 89.8, 87.3
LAPJV(test40)	⚪ NSD	1.04%	0.0144 → 0.0143, 0.0143
LAPJV(test400)	🟢 Faster!	6.78%	3.08 → 2.88, 2.87
MutualClusteringInfo(tr200)	⚪ NSD	-0.04%	717 → 706, 719
MutualClusteringInfo(tr50)	⚪ NSD	2.54%	510 → 491, 506
PathDist(postTrees)	⚪ NSD	-1.03%	3.58 → 3.58, 3.68
PhylogeneticInfoDistance(tr200)	🟣 ~same	3.3%	387 → 374, 374
PhylogeneticInfoDistance(tr50)	🟣 ~same	-2.26%	327 → 335, 332
RobinsonFoulds(tr200)	⚪ NSD	1.05%	2.67 → 2.64, 2.64
RobinsonFoulds(tr200)	⚪ NSD	1.29%	2.62 → 2.6, 2.57
RobinsonFoulds(tr50)	⚪ NSD	1.19%	4.39 → 4.33, 4.34

[codecov]

Codecov Report

❌ Patch coverage is 99.32886% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 99.31%. Comparing base (19accbb) to head (d606e94).
⚠️ Report is 27 commits behind head on main.

Files with missing lines	Patch %	Lines
src/nni_distance.cpp	99.32%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #165      +/-   ##
==========================================
+ Coverage   99.07%   99.31%   +0.24%     
==========================================
  Files          38       43       +5     
  Lines        2803     3205     +402     
==========================================
+ Hits         2777     3183     +406     
+ Misses         26       22       -4     

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[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
ClusteringInfoDistance(tr200)	🟣 ~same	0.94%	660 → 655, 651
ClusteringInfoDistance(tr50)	⚪ NSD	7.9%	369 → 341, 338
LAPJV(test2000)	⚪ NSD	6.51%	110 → 103, 104
LAPJV(test40)	⚪ NSD	-0.72%	0.014 → 0.014, 0.0142
LAPJV(test400)	🟢 Faster!	5.41%	3.19 → 3.01, 3.02
MutualClusteringInfo(tr200)	⚪ NSD	-0.49%	699 → 705, 692
MutualClusteringInfo(tr50)	⚪ NSD	1.52%	460 → 454, 453
PathDist(postTrees)	🟠 Slower 🙁	-42.31%	3.38 → 4.82, 4.81
PhylogeneticInfoDistance(tr200)	🟣 ~same	-2.28%	357 → 365, 365
PhylogeneticInfoDistance(tr50)	⚪ NSD	-1.89%	279 → 284, 284
RobinsonFoulds(tr200)	⚪ NSD	5.67%	2.52 → 2.37, 2.38
RobinsonFoulds(tr200)	⚪ NSD	-4.92%	2.22 → 2.33, 2.33
RobinsonFoulds(tr50)	⚪ NSD	-0.58%	3.84 → 3.86, 3.86

[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
ClusteringInfoDistance(tr200)	⚪ NSD	-0.58%	354 → 356, 357
ClusteringInfoDistance(tr50)	⚪ NSD	0.57%	317 → 317, 313
LAPJV(test2000)	🟣 ~same	-2.46%	81.2 → 84.1, 82.5
LAPJV(test40)	🟠 Slower 🙁	-8.35%	0.014 → 0.0155, 0.0145
LAPJV(test400)	🟣 ~same	-2.73%	2.83 → 2.9, 2.91
MutualClusteringInfo(tr200)	🟣 ~same	-3.07%	384 → 399, 394
MutualClusteringInfo(tr50)	🟠 Slower 🙁	-6.67%	402 → 427, 430
PathDist(postTrees)	⚪ NSD	-0.64%	3.53 → 3.58, 3.55
PhylogeneticInfoDistance(tr200)	⚪ NSD	0.04%	388 → 388, 386
PhylogeneticInfoDistance(tr50)	⚪ NSD	0.72%	330 → 324, 331
RobinsonFoulds(tr200)	⚪ NSD	-2.79%	2.59 → 2.67, 2.66
RobinsonFoulds(tr200)	⚪ NSD	4.25%	2.55 → 2.44, 2.46
RobinsonFoulds(tr50)	⚪ NSD	1.83%	4.23 → 4.13, 4.16

[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
ClusteringInfoDistance(tr200)	⚪ NSD	0.17%	356 → 355, 356
ClusteringInfoDistance(tr50)	⚪ NSD	-3.1%	304 → 314, 312
LAPJV(test2000)	🟣 ~same	-1.23%	82.4 → 83.8, 82.9
LAPJV(test40)	🟠 Slower 🙁	-7.72%	0.014 → 0.0153, 0.0148
LAPJV(test400)	🟣 ~same	-2.54%	2.83 → 2.9, 2.91
MutualClusteringInfo(tr200)	⚪ NSD	0.32%	393 → 391, 393
MutualClusteringInfo(tr50)	⚪ NSD	1.58%	419 → 408, 417
PathDist(postTrees)	⚪ NSD	1.14%	3.59 → 3.67, 3.54
PhylogeneticInfoDistance(tr200)	🟣 ~same	-1.54%	380 → 386, 387
PhylogeneticInfoDistance(tr50)	🟣 ~same	-1.92%	320 → 327, 325
RobinsonFoulds(tr200)	⚪ NSD	5.23%	2.77 → 2.59, 2.68
RobinsonFoulds(tr200)	⚪ NSD	0.57%	2.52 → 2.52, 2.45
RobinsonFoulds(tr50)	⚪ NSD	1.24%	4.24 → 4.22, 4.17