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

Open

ms609 wants to merge 31 commits into

claude/bremer-support-calculation-857d5f

Commits on Jul 9, 2026

feat(bremer): Bremer (decay) support via converse-constraint + pool

ms609
and
claude
committed
773eec1
fix(bremer): address red-team findings (scoring guard, reach, soundness)

ms609
and
claude
committed
02a7f7e
feat(bremer): parallelise per-clade converse searches over a cluster

ms609
and
claude
committed
952120e
fix(bremer): address self-review findings on the red-team fixes

ms609
and
claude
committed
2845b22

Commits on Jul 10, 2026

fix(bremer): guard converse sector/prune-reinsert against rebuilding the forbidden clade

ms609
and
claude
committed
c5f700b
fix(bremer): validate optimalScore, make censored attr consistent, strip pool-size overrides

ms609
and
claude
committed
8a0f56b
fix(bremer): make the scoring-mismatch guard a reliable warning, not a fuzzy error

ms609
and
claude
committed
22e6646
feat(bremer): record scoring provenance on MaximizeParsimony output; check it exactly in Bremer

ms609
and
claude
committed
9ee1d3c
test(bremer): cover zero-clade early return and pool-eviction score alignment

ms609
and
claude
committed
2cc6311
test(bremer): close TA-3/TA-4 via a search-injection seam

ms609
and
claude
committed
41556cd
Merge cpp-search into bremer-support-calculation

ms609
and
claude
committed
b26f948
fix(bremer): green the R CMD check (examples, spelling, docs, deps)

ms609
and
claude
committed
855c199
fix(bremer): make the runnable example cheap, seeded, and hang-proof

ms609
and
claude
committed
9a67c04
fix(bremer): run the example serially (nThreads = 1)

ms609
and
claude
committed
5387ec2

Commits on Jul 11, 2026

fix(bremer): serialize the SuboptimalTrees example too (nThreads = 1)

ms609
and
claude
committed
88cb280
fix(bremer): bound the pool example's search so --run-donttest can't hang

ms609
and
claude
committed
ba61fea
ci(probe): open a null graphics device before running plot-bearing examples

ms609
and
claude
committed
808c9aa
ci(probe): test the bgs-kernel hypothesis; portable gtimeout; add windows

ms609
and
claude
committed
b6d09ae
ci(probe): faithful one-process concatenated donttest repro with marker trail

ms609
and
claude
committed
3d4d660
ci(probe): localize the hang to a TreeLength sub-call; RNG vs C++-state discriminator

ms609
and
claude
committed
a6f61f6
ci(probe): per-pattern profile timing to localize the macOS profile hang

ms609
and
claude
committed
5a8e75c
ci: remove the donttest-hang debugging probe (investigation resolved by PR #272)

ms609
and
claude
committed
f255220

Commits on Jul 12, 2026

Commits on Jul 30, 2026

fix: replace deprecated .Dim and .Dimnames with dim and dimnames in structure()

ms609
and
claude
committed
78ee3d9

Commits on Aug 5, 2026

Merge branch 'cpp-search' into claude/bremer-support-calculation-857d5f

ms609
and
claude
committed
cc8d7d8
fix(bremer): address xhigh code-review findings

ms609
and
claude
committed
ed41dfc

Commits on Aug 18, 2026