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Surface headers for Linking To#190

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expose-lapjv
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Surface headers for Linking To#190
ms609 wants to merge 8 commits intotransfer-consensusfrom
expose-lapjv

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@ms609 ms609 commented Mar 20, 2026

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codecov bot commented Mar 20, 2026 •
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Codecov Report

❌ Patch coverage is 98.63014% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 95.75%. Comparing base (4a60427) to head (a5c20c1).

Files with missing lines Patch % Lines
inst/include/TreeDist/mutual_clustering_impl.h 95.89% 6 Missing ⚠️
Additional details and impacted files 
@@                  Coverage Diff                   @@
##           transfer-consensus     #190      +/-   ##
======================================================
- Coverage               95.76%   95.75%   -0.02%     
======================================================
  Files                      53       58       +5     
  Lines                    5267     5392     +125     
======================================================
+ Hits                     5044     5163     +119     
- Misses                    223      229       +6

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github-actions bot commented Mar 20, 2026 •
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⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call Status Change Time (ms)
ClusteringInfoDistance(tr200) ⚪ NSD 0.99% 15.5 →
15.4, 15.2
ClusteringInfoDistance(tr50) ⚪ NSD 3.27% 12 →
11.7, 11.5
LAPJV(test2000) 🟣 ~same -1.78% 91.9 →
93.5, 93.7
LAPJV(test40) 🟠 Slower 🙁 -5.96% 0.0148 →
0.0157, 0.0157
LAPJV(test400) 🟢 Faster! 4.11% 3.1 →
2.96, 2.97
MutualClusteringInfo(tr200) ⚪ NSD 2.51% 22 →
21.4, 21.5
MutualClusteringInfo(tr50) ⚪ NSD -0.27% 21.1 →
20.9, 21.7
PathDist(postTrees) ⚪ NSD 3% 3.4 →
3.33, 3.28
PhylogeneticInfoDistance(tr200) 🟣 ~same 0.53% 229 →
228, 229
PhylogeneticInfoDistance(tr50) 🟣 ~same 1.43% 78.3 →
77.3, 77
RobinsonFoulds(tr200) ⚪ NSD -1.01% 2.8 →
2.83, 2.82
RobinsonFoulds(tr200) ⚪ NSD -1.02% 2.59 →
2.63, 2.61
RobinsonFoulds(tr50) ⚪ NSD -0.75% 4.29 →
4.34, 4.29

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github-actions bot commented Mar 20, 2026 •
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⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call Status Change Time (ms)
ClusteringInfoDistance(tr200) 🟢 Faster! 9.83% 16.1 →
14.5, 14.4
ClusteringInfoDistance(tr50) ⚪ NSD -2.37% 10.3 →
10.4, 10.7
LAPJV(test2000) 🟠 Slower 🙁 -14.32% 100 →
114, 115
LAPJV(test40) 🟠 Slower 🙁 -9.67% 0.0143 →
0.0157, 0.0155
LAPJV(test400) 🟠 Slower 🙁 -5.7% 3.02 →
3.2, 3.18
MutualClusteringInfo(tr200) ⚪ NSD 5.57% 22.2 →
21, 20.9
MutualClusteringInfo(tr50) ⚪ NSD -1.94% 21.4 →
21.9, 21.7
PathDist(postTrees) 🟠 Slower 🙁 -38.89% 3.4 →
4.72, 4.72
PhylogeneticInfoDistance(tr200) 🟣 ~same 1.01% 232 →
229, 230
PhylogeneticInfoDistance(tr50) 🟢 Faster! 6.86% 74.5 →
69.4, 69.4
RobinsonFoulds(tr200) ⚪ NSD 0.34% 2.68 →
2.68, 2.66
RobinsonFoulds(tr200) ⚪ NSD -0.32% 2.39 →
2.42, 2.39
RobinsonFoulds(tr50) ⚪ NSD -0.89% 4.03 →
4.07, 4.05

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github-actions bot commented Mar 22, 2026 •
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⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call Status Change Time (ms)
ClusteringInfoDistance(tr200) ⚪ NSD 0.69% 15.7 →
15.6, 15.5
ClusteringInfoDistance(tr50) ⚪ NSD -0.02% 10.2 →
10.2, 10.3
LAPJV(test2000) 🟠 Slower 🙁 -21.73% 101 →
128, 121
LAPJV(test40) 🟠 Slower 🙁 -11.68% 0.0142 →
0.0159, 0.0159
LAPJV(test400) 🟠 Slower 🙁 -11.8% 3.04 →
3.42, 3.36
MutualClusteringInfo(tr200) ⚪ NSD -1.52% 21.9 →
21.9, 22.3
MutualClusteringInfo(tr50) ⚪ NSD -0.96% 21.2 →
21.4, 21.4
PathDist(postTrees) ⚪ NSD -1.3% 3.3 →
3.27, 3.36
PhylogeneticInfoDistance(tr200) 🟣 ~same 0.12% 235 →
234, 234
PhylogeneticInfoDistance(tr50) 🟣 ~same -2.01% 71.6 →
72.4, 73.3
RobinsonFoulds(tr200) ⚪ NSD 0.47% 2.66 →
2.65, 2.65
RobinsonFoulds(tr200) ⚪ NSD 0.66% 2.38 →
2.39, 2.36
RobinsonFoulds(tr50) ⚪ NSD -0.25% 4 →
4.03, 3.98

@ms609
Fix LAPJV alignment regression + coverage for mutual_clustering_impl.h
8d7f116 
lap_impl.h: add __attribute__((optimize("align-functions=64",
"align-loops=16"))) on lap() (GCC only) to stabilise instruction
alignment across TU layout changes.

cost_matrix.h: add setWithTranspose() and markTransposed() methods.

lap.cpp: use combined fill+transpose in lapjv() to eliminate the extra
makeTranspose() O(n²) pass introduced by the header refactor.

tree_distance_functions.cpp: add cpp_mci_impl_score() wrapper that calls
TreeDist::mutual_clustering_score() from the installable header, covering
find_exact_matches_raw() and the MCI score computation.

test-mci_impl.R: exercises exact-match early exit and partial-match + LAP
paths through the header implementation.
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github-actions bot commented Mar 22, 2026 •
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⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call Status Change Time (ms)
ClusteringInfoDistance(tr200) 🟢 Faster! 7.02% 15.6 →
14.5, 14.6
ClusteringInfoDistance(tr50) ⚪ NSD -4.63% 10.1 →
10.6, 10.7
LAPJV(test2000) 🟠 Slower 🙁 -9.78% 109 →
119, 119
LAPJV(test40) 🟠 Slower 🙁 -5.36% 0.0143 →
0.015, 0.0151
LAPJV(test400) 🟠 Slower 🙁 -9.19% 3.11 →
3.42, 3.35
MutualClusteringInfo(tr200) 🟢 Faster! 5.28% 22 →
20.8, 20.7
MutualClusteringInfo(tr50) ⚪ NSD -1.41% 21.4 →
21.7, 21.7
PathDist(postTrees) ⚪ NSD 1.15% 3.31 →
3.27, 3.28
PhylogeneticInfoDistance(tr200) 🟣 ~same 0.18% 234 →
234, 233
PhylogeneticInfoDistance(tr50) 🟠 Slower 🙁 -5.9% 71.9 →
76.3, 76
RobinsonFoulds(tr200) ⚪ NSD 1.97% 2.69 →
2.64, 2.64
RobinsonFoulds(tr200) ⚪ NSD 1.85% 2.41 →
2.37, 2.35
RobinsonFoulds(tr50) ⚪ NSD 1.36% 4.05 →
4.02, 3.97

@ms609
Move -I../inst/include to PKG_CPPFLAGS
a5c20c1 
PKG_CXXFLAGS is overridden by ASAN/ubsan ~/.R/Makevars on CI,
dropping the inst/include path.  PKG_CPPFLAGS is not overridden.
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github-actions bot commented Mar 22, 2026

Performance benchmark results

Call Status Change Time (ms)
ClusteringInfoDistance(tr200) 🟣 ~same -3.87% 15.2 →
15.6, 16
ClusteringInfoDistance(tr50) ⚪ NSD 0% 12.4 →
12.5, 12.2
LAPJV(test2000) 🟠 Slower 🙁 -15.51% 90.8 →
106, 104
LAPJV(test40) 🟠 Slower 🙁 -6.72% 0.0146 →
0.0155, 0.0157
LAPJV(test400) 🟠 Slower 🙁 -4.93% 2.93 →
3.08, 3.06
MutualClusteringInfo(tr200) ⚪ NSD -1.32% 23.4 →
23.4, 23.7
MutualClusteringInfo(tr50) ⚪ NSD 1.27% 25.6 →
25.4, 25.2
PathDist(postTrees) ⚪ NSD 2.79% 3.55 →
3.48, 3.4
PhylogeneticInfoDistance(tr200) ⚪ NSD 2.88% 248 →
240, 241
PhylogeneticInfoDistance(tr50) 🟣 ~same -2.38% 79 →
81, 80.6
RobinsonFoulds(tr200) ⚪ NSD -0.83% 2.97 →
3, 2.98
RobinsonFoulds(tr200) ⚪ NSD -0.98% 2.73 →
2.74, 2.77
RobinsonFoulds(tr50) ⚪ NSD -1.24% 4.54 →
4.58, 4.6

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