asm popcounts

[ms609]

Speeds up tight loops

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.33%. Comparing base (a13532f) to head (7169b3a).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #256   +/-   ##
=======================================
  Coverage   96.32%   96.33%           
=======================================
  Files          77       77           
  Lines        5749     5750    +1     
=======================================
+ Hits         5538     5539    +1     
  Misses        211      211           

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[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
as.Splits(bigTrees)	⚪ NSD	7.86%	26.2 → 25.5, 21.9
as.Splits(someTrees)	⚪ NSD	-3.46%	11.7 → 12.2, 11.6
Consensus(forest1k.888, check = FALSE)	⚪ NSD	-1.08%	98.6 → 101, 98.6
Consensus(forest201.80, check = FALSE)	⚪ NSD	3.36%	4.34 → 4.23, 4.17
Consensus(forest21.260, 0.5, FALSE)	⚪ NSD	3.22%	1.29 → 1.24, 1.25
Consensus(forest21.260)	⚪ NSD	7.18%	1.35 → 1.25, 1.27
Consensus(forestMaj, 0.5, FALSE)	⚪ NSD	-1.4%	2.97 → 3, 3.04
DropTip(tr2000, 5)	⚪ NSD	12.28%	20.3 → 17.8, 17.8
DropTip(tr80, 5)	⚪ NSD	2.46%	0.111 → 0.108, 0.108
DropTip(unlen2k, 5)	⚪ NSD	1.96%	0.219 → 0.222, 0.209
DropTip(unlen80, 5)	⚪ NSD	3.69%	0.0423 → 0.0413, 0.0402
lapply(bigSplits, as.phylo)	🟣 ~same	3.26%	30.8 → 29.8, 29.8
lapply(someSplits, as.phylo)	⚪ NSD	0.34%	14.4 → 14.5, 14
PathLengths(tr2000, full = TRUE)	⚪ NSD	0.52%	17.7 → 17.4, 17.7
PathLengths(tr80, full = TRUE)	🟠 Slower 🙁	-275.03%	0.0306 → 0.117, 0.0437
PathLengths(tr80Unif, full = TRUE)	⚪ NSD	-30.29%	0.0325 → 0.118, 0.0394
RootTree(tr2000, 5)	⚪ NSD	-2.52%	0.387 → 0.409, 0.386
RootTree(tr80, c("t3", "t36"))	⚪ NSD	-0.07%	0.0726 → 0.0742, 0.0714
RootTree(tr80, "t3")	⚪ NSD	-1.19%	0.0505 → 0.0513, 0.0509
RootTree(tr80, "t30")	⚪ NSD	-1.53%	0.0509 → 0.0524, 0.0512
RootTree(unlen2k, 5)	⚪ NSD	0.33%	0.336 → 0.331, 0.34
RootTree(unlen80, c("t3", "t36"))	⚪ NSD	-1.94%	0.0655 → 0.0668, 0.0668
RootTree(unlen80, "t3")	⚪ NSD	-0.52%	0.0445 → 0.0456, 0.0443
RootTree(unlen80, "t30")	⚪ NSD	-1.39%	0.0445 → 0.046, 0.0446
TreeDist::RobinsonFoulds(forest201.80)	⚪ NSD	18.65%	20.1 → 16.3, 16.4
TreeDist::RobinsonFoulds(forest21.888)	⚪ NSD	11.48%	3.79 → 3.36, 3.35
TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)	⚪ NSD	-2.42%	0.106 → 0.106, 0.112
TreeTools:::postorder_order(bal40)	⚪ NSD	0.62%	0.00177 → 0.00174, 0.00177
TreeTools:::postorder_order(bal40k)	⚪ NSD	-0.09%	0.436 → 0.436, 0.437
TreeTools:::postorder_order(dbal40)	⚪ NSD	1.05%	0.0019 → 0.00188, 0.00188
TreeTools:::postorder_order(dbal40k)	⚪ NSD	-0.28%	2.39 → 2.42, 2.38
TreeTools:::postorder_order(dpec40)	⚪ NSD	0.93%	0.00312 → 0.0031, 0.00309
TreeTools:::postorder_order(dpec40k)	🟣 ~same	-0.21%	3610 → 3620, 3620
TreeTools:::postorder_order(drnd80)	⚪ NSD	0.58%	0.00518 → 0.00519, 0.00513
TreeTools:::postorder_order(nbal40)	⚪ NSD	1.33%	0.00226 → 0.00222, 0.00224
TreeTools:::postorder_order(nbal40k)	⚪ NSD	-2%	2.41 → 2.44, 2.57
TreeTools:::postorder_order(npec40)	⚪ NSD	0.88%	0.0034 → 0.00336, 0.00338
TreeTools:::postorder_order(npec40k)	🟣 ~same	-0.31%	3630 → 3640, 3640
TreeTools:::postorder_order(nrnd80)	⚪ NSD	0.89%	0.00573 → 0.0057, 0.00565
TreeTools:::postorder_order(pec40)	⚪ NSD	1.69%	0.00177 → 0.00174, 0.00172
TreeTools:::postorder_order(pec40k)	⚪ NSD	-0.54%	0.432 → 0.436, 0.433
TreeTools:::postorder_order(rnd80)	⚪ NSD	4.05%	0.00222 → 0.00218, 0.00211