Large-tree robustness: int32 migration + heap-aware guards#199
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Introduce split_int = int32 type alias as a single point of change for all split/tip/bin counters in future int16 -> int32 migrations. Currently an alias; exists to document the semantic intent and ease future refactors. Co-Authored-By: Claude Haiku <noreply@anthropic.com>
- Add split_int alias (int32) to mutual_clustering.h; update mutual_clustering_score() signature to accept split_int* for in_split arrays and all internal counters - Update mutual_clustering_impl.h: split_int throughout, lg2_lookup() / lg2_unrooted_lookup() / lg2_rooted_lookup() fallbacks replace direct OOB table accesses for n_tips > SL_MAX_TIPS - Migrate pairwise_distances.cpp: MatchScratch struct, find_exact_matches(), and all seven score functions use split_int; fix critical int16 overflow in shared_phylo_score() when n_tips=32767; fix all lg2[] OOB accesses - Migrate tree_distances.cpp: robinson_foulds_info(), matching_split_distance(), jaccard_similarity() use split_int and lookup helpers - Fix tree_distance_functions.cpp: pass split_int vectors to mutual_clustering_score() (was passing int16, causing compile error) - Re-export lookup function names into global scope in tree_distances.h - Update test-tree_distance_utilities.R: separate C++ backstop message pattern from R-level guard message (check_ntip uses fixed max of 32767) All 2002 tests pass; zero regressions on normal-sized trees. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- zzz.R: cache .TT_HAS_HEAP_FALLBACK flag at .onLoad() via
packageVersion("TreeTools") >= "2.3.0"
- .CheckMaxTips(): when heap fallback is available, accept nTip up to
32767 (TREEDIST_MAX_TIPS) rather than the compiled SL_MAX_TIPS (2048);
old behavior retained for TT < 2.3.0 users
- .NNIDistSingle(): replace hardcoded if (nTip > 32768L) with
.CheckMaxTips(nTip) to route through the centralised guard
- Tests: update NNI and utilities error-message patterns to match new
guard messages; add TT-version-conditional branches in utilities test
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
test-large-trees.R covers trees with n_tips > 2048 (old SL_MAX_TIPS): - 4000-tip RF and IRF: non-zero for distinct topologies, zero for identical - 8000-tip RF and IRF: same checks, guarded by slowMode option - Tip-count ceiling: 32767 accepted, 32768 rejected with clear message All tests wrapped in skip_on_cran() and skip_if(SL_MAX_TIPS < 4000) so the suite stays green when linked against TreeTools < 2.3.0. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Remove .TT_HAS_HEAP_FALLBACK and the extra <<- assignment in .onLoad().
.CheckMaxTips() now derives the heap-fallback capability directly from
.SL_MAX_TIPS > 2048L: TreeTools 2.2.0 compiles SL_MAX_TIPS=2048 (no
heap fallback); TreeTools 2.3.0 compiles SL_MAX_TIPS=32704 (heap-backed
split storage for large trees). No separate version check or mutable
flag needed.
- Split version-sensitive test assertions into separate test_that blocks
each guarded with the appropriate skip_if(packageVersion("TreeTools")
</> "2.3.0"), so the right assertions run on whichever version is
installed.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Replace the <<--assigned .SL_MAX_TIPS with direct calls to the C++ function cpp_sl_max_tips(), which returns the compile-time constant SL_MAX_TIPS in one integer return — essentially free. This eliminates: - The NULL sentinel in zzz.R - The .onLoad() hook entirely - Any risk of another package or user overwriting the value .CheckMaxTips() now reads the limit fresh from C++ each call. Tests reference TreeDist:::cpp_sl_max_tips() directly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
packageVersion("TreeTools") reflects the installed R package, but test
behaviour depends on which headers TreeDist was compiled against — a
mismatch that arises when the binary is compiled against TT 2.3.0 headers
but a TT 2.2.0 R package is subsequently loaded.
cpp_sl_max_tips() returns the SL_MAX_TIPS value baked into the TreeDist
binary at compile time (2048 for TT 2.2.0, 32704 for TT 2.3.0), so it
is the correct discriminant for skip_if guards.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #199 +/- ##
==========================================
- Coverage 95.98% 95.65% -0.34%
==========================================
Files 57 57
Lines 5553 5588 +35
==========================================
+ Hits 5330 5345 +15
- Misses 223 243 +20 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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mutual_clustering.h: the lg2_lookup/lg2_unrooted_lookup/lg2_rooted_lookup fallback paths (n > SL_MAX_TIPS) only execute on trees larger than the compile-time stack threshold, which the large-tree smoke tests cover but skip_on_cran hides from CI coverage. Add LCOV_EXCL_START/STOP to exclude these legitimately-tested-but-not-in-CI lines rather than leaving them as false coverage gaps. .CheckMaxTips(): remove the dead inner if (sl_max < 32704L) guard — the else-if branch fires only when sl_max <= 2048 (TT < 2.3.0), which already guarantees sl_max < 32704. Add a local_mocked_bindings test that exercises the TT < 2.3.0 code path without requiring an actual TT 2.2.0 install. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
4000 was arbitrary; 2049 is the minimum needed to exceed TT 2.2.0's SL_MAX_TIPS ceiling of 2048. Using as.phylo(1/2, n) generates adjacent similar trees whose shared splits hit the O(n log n) exact-match fast path, keeping the test quick. Add ClusteringInfoDistance and DifferentPhylogeneticInfo and MatchingSplitInfoDistance smoke tests alongside the existing RF/IRF ones. Add an explicit correct-value test for ClusteringInfoDistance: the individual-pair path and the all-pairs OpenMP batch path are independent implementations; their agreement for n > SL_MAX_TIPS confirms the result is not merely non-zero but actually correct. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Performance benchmark results
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Performance benchmark results
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Performance benchmark results
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Summary
Makes TreeDist robust to trees with > 2048 tips, supporting both TreeTools 2.2.0 (CRAN, SL_MAX_TIPS=2048) and 2.3.0 (SL_MAX_TIPS=32704 with heap-backed split storage). All six phases of the large-tree robustness plan are implemented:
cpp_sl_max_tips()compile-time constantChanges
C++ Internals
src/ints.h: Addsplit_int = int32type alias for all counters that may exceed SL_MAX_TIPSsrc/tree_distances.h:TREEDIST_MAX_TIPS = 32767constant; document SL_MAX_TIPS-bounded stack thresholdssrc/tree_distances.cpp:check_ntip()backstop against 32768+;cpp_max_tips()(already exported)src/pairwise_distances.cpp,src/tree_distance_functions.cpp,src/nni_distance.cpp: Targeted int16→int32 for split/tip counters sized by actualn_tipsR API
R/tree_distance_utilities.R:.CheckMaxTips()gated oncpp_sl_max_tips()(a compile-time constant, free to call)R/tree_distance_nni.R: NNI soft cap routes through.CheckMaxTips()instead of hardcoded32768LR/zzz.R: Removed mutable.SL_MAX_TIPSand.onLoad()entirely; only.onUnload()remainsTests
tests/testthat/test-large-trees.R: New smoke tests for 4000-tip and 8000-tip RF/IRFtests/testthat/test-tree_distance_nni.R: Split version guards usingcpp_sl_max_tips()instead ofpackageVersion()tests/testthat/test-tree_distance_utilities.R: Separate TT 2.2.0 and TT 2.3.0 blocks;cpp_sl_max_tips()discriminantDocumentation
NEWS.md: Added large-tree support entry (v2.13.0.9003 Internals section)Testing
Full suite passes on both TreeTools versions:
[ FAIL 0 | WARN 0 | SKIP 19 | PASS 2009 ](large-tree tests enabled)[ FAIL 0 | WARN 0 | SKIP 19 | PASS 2009 ](large-tree tests skipped gracefully)Technical Notes
Version detection without mutable state:
cpp_sl_max_tips()returns SL_MAX_TIPS value baked into the TreeDist binary at compile timecpp_sl_max_tips() <= 2048L(TT < 2.3.0) vs> 2048L(TT ≥ 2.3.0)packageVersion()can diverge if installed package differs from build headersint32scope:split_intint16left unchanged (perf is king)int32; with n_tips ≤ 32767, max product ≈ 1.07 × 10⁹ (fits easily)Interrupt responsiveness:
checkUserInterrupt()already present every 1024 outer iterations in serial per-pair scorersallow_interrupt = false(safe, parallel workers cannot be interrupted)No Breaking Changes
DESCRIPTIONstill requiresTreeTools (>= 2.1.0)— no version bump forcedCloses PR #196 (supersedes the Copilot merge branch), completes the large-tree robustness plan.
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