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Bremer (decay) support via converse-constraint + pool - #270

Merged

ms609 merged 69 commits into

cpp-searchfrom

claude/bremer-support-calculation-857d5f

Sep 8, 2026

Merged

Bremer (decay) support via converse-constraint + pool#270
ms609 merged 69 commits into
cpp-searchfrom
claude/bremer-support-calculation-857d5f

Commits on Jul 9, 2026
- feat(bremer): Bremer (decay) support via converse-constraint + pool
  
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- fix(bremer): address red-team findings (scoring guard, reach, soundness)
  
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- feat(bremer): parallelise per-clade converse searches over a cluster
  
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- fix(bremer): address self-review findings on the red-team fixes
  
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Commits on Jul 10, 2026
- fix(bremer): guard converse sector/prune-reinsert against rebuilding the forbidden clade
  
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- fix(bremer): validate optimalScore, make censored attr consistent, strip pool-size overrides
  
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- fix(bremer): make the scoring-mismatch guard a reliable warning, not a fuzzy error
  
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- feat(bremer): record scoring provenance on MaximizeParsimony output; check it exactly in Bremer
  
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- test(bremer): cover zero-clade early return and pool-eviction score alignment
  
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- test(bremer): close TA-3/TA-4 via a search-injection seam
  
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- Merge cpp-search into bremer-support-calculation
  
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- fix(bremer): green the R CMD check (examples, spelling, docs, deps)
  
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- fix(bremer): make the runnable example cheap, seeded, and hang-proof
  
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- fix(bremer): run the example serially (nThreads = 1)
  
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Commits on Jul 11, 2026
- fix(bremer): serialize the SuboptimalTrees example too (nThreads = 1)
  
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  88cb280
- fix(bremer): bound the pool example's search so --run-donttest can't hang
  
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- ci(probe): open a null graphics device before running plot-bearing examples
  
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- ci(probe): test the bgs-kernel hypothesis; portable gtimeout; add windows
  
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- ci(probe): faithful one-process concatenated donttest repro with marker trail
  
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- ci(probe): localize the hang to a TreeLength sub-call; RNG vs C++-state discriminator
  
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- ci(probe): per-pattern profile timing to localize the macOS profile hang
  
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- ci: remove the donttest-hang debugging probe (investigation resolved by PR #272)
  
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Commits on Jul 12, 2026
- Merge branch 'cpp-search' into claude/bremer-support-calculation-857d5f
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- Merge branch 'cpp-search' into claude/bremer-support-calculation-857d5f
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Commits on Jul 30, 2026
- fix: replace deprecated .Dim and .Dimnames with dim and dimnames in structure()
  
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Commits on Aug 5, 2026
- Merge branch 'cpp-search' into claude/bremer-support-calculation-857d5f
  
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- fix(bremer): address xhigh code-review findings
  
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Commits on Aug 18, 2026
- Merge branch 'main' into claude/bremer-support-calculation-857d5f
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- Merge current Bremer work (ed41dfcea) into the PR branch
  
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- Merge cpp-search into claude/bremer-support-calculation-857d5f
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- Merge cpp-search into claude/bremer-support-calculation-857d5f
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Commits on Sep 7, 2026
- Merge branch 'cpp-search' into claude/bremer-support-calculation-857d5f
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Commits on Sep 8, 2026
- Suboptimality → SuboptimalTrees.R
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- ise→ize
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- cache
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- ucfirst
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- Tighten doc
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- Brand loyalty
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- Update test-Bremer.R
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- TreeTools::Consensus
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- ren
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- Redoc; inheritParams
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- rm Bremer's `cl`
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- roxygen 8.1.0
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- rm babble
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- ws
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- explanation
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- no warning
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- no chat if verb = 0
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- expect_silent
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- No message, just warn
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- ds→vinther
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- ssh
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- silence
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- hush
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- hush
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- Capture output
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- Examples
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- maxSeconds; mcSamples
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- Merge branch 'ms609-approximation-time-budget' into claude/bremer-support-calculation-857d5f
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- document
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- slim
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- TT 2.4.0.9002
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- extra-repositories
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- Get TreeTools?
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- tighten needs
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- Comment out unregistered DOI
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- Simply use remotes; cache-1 is gone
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- missing ,
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Commits

Commits on Jul 9, 2026

Commits on Jul 10, 2026

Commits on Jul 11, 2026

Commits on Jul 12, 2026

Commits on Jul 30, 2026

Commits on Aug 5, 2026

Commits on Aug 18, 2026

Commits on Sep 7, 2026

Commits on Sep 8, 2026