Land #217 (exact DuckDB counts) on main, and fix the Wald tail by hyperpolymath · Pull Request #226 · hyperpolymath/MetaManifold-WebUI

hyperpolymath · 2026-10-23T07:40:47Z

What this is

#217 (fix(stats): aggregate DuckDB counts exactly) has been CONFLICTING
since main moved: #218 fixed the same run-summaries 500 independently, #210
repaired the differential/analysis modules, #220 removed the Evidence UI, and
#222 repaired the CladeCumulus tree/route code. This branch merges the current
main into #217's head, resolves every conflict, and repairs the two main-line
defects that were failing the required Julia tests check on both branches.
It contains #217's content in full, so merging it lands #217.

Conflict resolution (4 files)

src/server/routes/validated_statistics.jl — the PR's implementation is
kept unchanged. Main's Fix validated-statistics run summaries 500 (invalid GROUP BY aggregation) #218 kept a GROUP BY-free ORDER BY … LIMIT MAX_CELLS+1 window and scanned only the counts member for float tokens;
fix(stats): aggregate DuckDB counts exactly #217 streams the raw rows, bounds features/cells as rows arrive, and scans
the whole direct body. Nothing main added after 7bb716d was lost: the two
versions differed only in those four hunks.
test/unit/test_validated_statistics.jl — union. Main's (1.5, -1, 2^53+1)
Dict cases and its 1.0/1e0 raw-token loop are kept next to fix(stats): aggregate DuckDB counts exactly #217's
byte-backed Vector{UInt8} cases and its round_digits: 8.0 rejection, so
both sides' contracts are now tested.
test/unit/test_exact_summaries.jl — main's wording; same assertions.
.github/workflows/ci.yml — main's log path/title with fix(stats): aggregate DuckDB counts exactly #217's ordering that
runs the validated-statistics suite first.

The CladeCumulus merge takes main's #222 implementation (real tables only
via duckdb_tables(), SubString normalisation at the request boundary, NHX
capture, PLACEMENT_WEIGHT_SUM_TOL = 0.05) and keeps the two repairs #222
still lacks: PhyloNode.edge_number in _graft_jplace_queries (main reads a
field that does not exist) and the connecting branch in
_reaggregate_after_move, so a subtree PD agrees with clade_faith_pd.

Two main-line fixes needed to get the required checks green

UndefVarError: erfc — CompositionalModels._wald called erfc
without importing or defining it, so every multinomial / Dirichlet-
multinomial fit raised on any tree where it could load. The module states it
carries its own special functions so the models add no dependency, so
_erfc is added in the same style: erfc(t) = Q(1/2, t²), power series
below the switch, continued fraction above it (modified Lentz).
DifferentialConfig(…, min_prevalence=1.0) — the test passed
min_prevalence as a keyword; it is positional in the constructor and in
the route that builds it. Fixed in the test.

Validation

DuckDB (independent of Julia): the old grouped query fails with
column "s1" must appear in the GROUP BY clause…; the streamed query returns
G → [3, 2^127], H → [4, 1], and the prefix=s2 + Pident ≥ 99 filter
returns s2 → 2^126, exactly the values the tests assert.
The integer-token scanner was ported line-for-line and run over the test
bodies: 1.0, 1e0, 3.0e-1 and round_digits: 8.0 are refused; integer
tokens, quoted "1.0", escapes and digits inside strings are accepted; the
run route (which legitimately takes Pident: 99.0) is not scanned.
_erfc was checked against libm's erfc on t ∈ [0, 30]: worst relative
error 1.5e-13, and the two-sided tail reproduces this file's p-value
references to 1.5e-12 (the test asserts rtol = 1e-6).
All 122 src/**.jl and test/**.jl files parse with a Julia grammar; the
three files that still show grammar nodes (remote_exec.jl,
occupancy_disagreement_test.jl, test_determinism.jl) are untouched here.
git diff --check clean; .github/workflows/ci.yml parses as YAML.
Julia itself is not installable in this sandbox (the toolchain download host
is blocked), so the pinned suite has to be the authority: this PR exists to
give CI the merged tree to run on.

Relationship to #217

Merging this lands #217's content. To make #217 itself mergeable instead, its
head must be advanced to this branch; that is a single command for someone who
can push to it:

git push origin arena/a8928088-metamanifold-webui:arena/dd990535-metamanifold-webui

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui # Conflicts: # frontend/src/api/types.ts # frontend/src/components/PipelineStages.test.ts # frontend/src/components/differentialTable.ts # frontend/src/views/StudyView.tsx # test/unit/test_numeric_policy.jl Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>

…idation

Resolve the conflicts between fix(stats): aggregate DuckDB counts exactly (arena/dd990535) and main since 7bb716d. - src/server/routes/validated_statistics.jl: keep the PR's implementation. Main's #218 fixed the same 500 with an ORDER BY + LIMIT window and a counts-only token scan; the PR supersedes it with a streamed query that bounds features/cells as rows arrive and with a whole-body integer-token scan, so the file is taken from the PR unchanged. - test/unit/test_validated_statistics.jl: union of both sides. Main's (1.0, 1.5, -1, 2^53+1) Dict cases and decimal/exponent raw token cases are kept alongside the PR's byte-backed request-body cases and its 8.0 policy rejection. - test/unit/test_exact_summaries.jl: main's wording, same assertions. - .github/workflows/ci.yml: main's log path and error title, with the PR's ordering that runs the validated-statistics suite first. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

#222 fixes the same CladeCumulus defects as this PR's d5f8060 and adds the route/loading repairs on top, so the clade conflicts take main's wording and main's extra fixes. The PR's remaining semantic repairs are kept because main still carries them: - `PhyloNode.edge_number` in `_graft_jplace_queries` (main still reads the non-existent `edge_num` field there); - the connecting branch in `_reaggregate_after_move`, so a subtree PD agrees with `clade_faith_pd`. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

`_wald` called `erfc`, which `CompositionalModels` never imported or defined: every multinomial and Dirichlet-multinomial fit raised `UndefVarError`, so five Differential testsets errored on any tree where they could load at all. The module deliberately carries its own special functions ("so the models add no dependency"), so `_erfc` follows the same pattern: erfc(t) = Q(1/2, t^2), the power series below the switch and the continued fraction above it, in the modified-Lentz form. Measured against libm's erfc over t in [0, 30], the worst relative error is 1.5e-13, and the two-sided tail reproduces the p-value reference values in test/unit/test_differential.jl to 1.5e-12. Also fix a test that had never been run to completion: it passed `min_prevalence` as a keyword to `DifferentialConfig`, which takes it positionally (as the route does). Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

coderabbitai · 2026-10-23T07:40:57Z

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.github/workflows/ci.yml
src/analysis/clade_cumulus.jl
src/analysis/compositional.jl
src/pipeline/phylogeny.jl
src/server/routes/clade_cumulus.jl
src/server/routes/validated_statistics.jl
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chatgpt-codex-connector · 2026-10-23T07:40:58Z

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-23T07:55:18.721636Z	`0cb9f37`	New commits

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github-actions · 2026-10-23T07:41:51Z

Fork governance

Lane	Status	Run
DEED syntax (repo deed)	🟢 conformant	run 39924505449
Hypatia verdict grid	purple (job: success)	same run

🟣 critical · commit 8de1d0b70f65 · run 39924505449

Reporter	Status	Critical	High	Medium	Since previous revision
Hypatia scan	🟣 critical	43	59	31	↔ unchanged
panic-attack assail	🔴 high	0	6	13	↔ unchanged
pons asinorum	🟡 medium	0	0	10	↔ unchanged
rhodibot (RSR compliance)	🟠 indeterminate	0	0	0	— indeterminate
panicbot (panic recovery, error handling)	🟠 indeterminate	0	0	0	— indeterminate
echidnabot (formal verification: proofs/)	🟠 indeterminate	0	0	0	— indeterminate
seambot (integration health: API routes)	🟠 indeterminate	0	0	0	— indeterminate
finishingbot (release readiness)	🟠 indeterminate	0	0	0	— indeterminate
accessibilitybot (WCAG on the React UI)	🟠 indeterminate	0	0	0	— indeterminate
glambot (presentation quality)	🟠 indeterminate	0	0	0	— indeterminate
cipherbot	⚪ not applicable	0	0	0	↔ unchanged
sustainabot	⚪ not applicable	0	0	0	↔ unchanged

Hypatia scan: 133 finding(s)

critical cicd_rules/banned_language_file — frontend/src/views/run/parseFilterYaml.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/encode.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/charts.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/export.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/figure.test.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/legend.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/types.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/download.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/text.test.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/timeago.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/text.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useUnsavedGuard.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useApi.test.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useApi.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useAnalysis.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useSSE.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useTabParam.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useNavRefresh.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useJobEvents.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/about.ts — TypeScript file detected -- banned language
113 more; see the structured report in the artifact.

panic-attack assail: 19 finding(s)

high DynamicCodeExecution — src/pipeline/dada2/context.jl — eval/Meta.parse in src/pipeline/dada2/context.jl
high DynamicCodeExecution — src/analysis/analysis.jl — eval/Meta.parse in src/analysis/analysis.jl
high DynamicCodeExecution — src/analysis/differential.jl — eval/Meta.parse in src/analysis/differential.jl
high DynamicCodeExecution — src/core/provenance.jl — eval/Meta.parse in src/core/provenance.jl
high DynamicCodeExecution — scripts/check-julia-syntax.jl — eval/Meta.parse in scripts/check-julia-syntax.jl
high DynamicCodeExecution — test/unit/test_permanova.jl — eval/Meta.parse in test/unit/test_permanova.jl
medium UnsafeFFI — src/core/memory_probe.jl — 3 ccall/FFI calls in src/core/memory_probe.jl
medium InputBoundary — src/server/routes/runs.jl — 2 JSON3.read/JSON.parse call(s) with 0 try block(s) in src/server/routes/runs.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — src/server/routes/composition.jl — 6 JSON3.read/JSON.parse call(s) with 2 try block(s) in src/server/routes/composition.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — src/server/routes/studies.jl — 4 JSON3.read/JSON.parse call(s) with 2 try block(s) in src/server/routes/studies.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — src/server/routes/analysis.jl — 9 JSON3.read/JSON.parse call(s) with 4 try block(s) in src/server/routes/analysis.jl — these throw on malformed input; wrap in try/catch
medium UnsafeFFI — install.jl — 1 ccall/FFI calls in install.jl
medium ProofDrift — test/unit/test_occupancy_grade.jl — 2 `@test x isa Y` assertion(s) with no value check — type-only tests may substitute for an unwritten formal theorem in test/unit/test_occupancy_grade.jl
medium ProofDrift — test/unit/test_evidence.jl — 1 `@test x isa Y` assertion(s) with no value check — type-only tests may substitute for an unwritten formal theorem in test/unit/test_evidence.jl
medium InputBoundary — bench/advanced_zero_handling/benchmark.jl — 1 JSON3.read/JSON.parse call(s) with 0 try block(s) in bench/advanced_zero_handling/benchmark.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — frontend/src/figure/charts.ts — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/figure/charts.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
medium InputBoundary — frontend/src/tree/model.ts — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/tree/model.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
medium InputBoundary — frontend/src/api/events.ts — 2 JSON.parse call(s) with 0 try block(s) in frontend/src/api/events.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
medium InputBoundary — frontend/src/components/alphaMetrics.tsx — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/components/alphaMetrics.tsx — JSON.parse throws SyntaxError on malformed input; wrap in try-catch

pons asinorum: 10 finding(s)

medium string-concat-in-loop — ./frontend/src/tree/model.ts:122 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/model.ts:118 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:69 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:66 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:61 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:53 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:43 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:42 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium unreachable-after-jump — ./frontend/src/figure/PaneEditor.tsx:45 — statement is unreachable after an unconditional jump (T0, HEURISTIC)
medium unreachable-after-jump — ./frontend/src/components/PublicationTablesPanel.tsx:208 — statement is unreachable after an unconditional jump (T0, HEURISTIC)

rhodibot (RSR compliance): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

panicbot (panic recovery, error handling): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

echidnabot (formal verification: proofs/): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

seambot (integration health: API routes): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

finishingbot (release readiness): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

accessibilitybot (WCAG on the React UI): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

glambot (presentation quality): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

cipherbot: not_applicable — no cryptography is implemented in this repository

⚪ not applicable: no cryptography is implemented in this repository

sustainabot: not_applicable — fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)

⚪ not applicable: fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)

Scope: static findings reported by each row's tool at the named commit. Purple, red, yellow and blue grade the worst finding present; orange is evidence missing, malformed or a scanner that did not run; grey is an explicit scope exclusion with its reason. No row is a security certification. report.json, badge.json and the raw findings are in the verdict-grid artifact on the linked run.

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chatgpt-codex-connector · 2026-10-23T07:45:25Z

        end
+        # Match clade_faith_pd: an active non-root clade includes the branch
+        # connecting it to its parent as well as its active descendant branches.
+        any_active && !is_root && (sub_pd += max(0.0, u.branch_length))


Avoid double-counting internal branches after a move

When an accepted drag-and-drop proposal has an active internal child, this addition puts that child's incoming branch into rk.subtree_pd, but the parent still adds rk.branch_length + rk.subtree_pd at line 1820. Consequently every active non-root internal edge is counted twice in the proposed tree—for example, a 0.3 internal branch with a 0.1 tip branch contributes 0.7 at the root instead of 0.4—corrupting the displayed and persisted subtree PD. The recursion needs one consistent invariant: either child subtree_pd includes its incoming branch and parents add only that value, or parents remain responsible for adding child branches.

Useful? React with 👍 / 👎.

Correct — and now fixed in 0cb9f37. The addition at the node and the parent's rk.branch_length + rk.subtree_pd were two conventions in one pass, so every active non-root internal edge was counted twice.

subtree_pd is now node-local throughout, which is the convention clade_faith_pd already uses in the build path: a leaf puts its own branch into the value it returns, and the parent adds only rk.subtree_pd. Verified by running both recursions over 800 random trees — the patched form agrees with clade_faith_pd exactly, the previous form disagreed on 409 of them.

Codex review (P2) on #226: `_reaggregate_after_move` added a clade's own branch at the node and its parent also added `rk.branch_length`, so every active non-root internal edge was counted twice in a proposed tree. Make `subtree_pd` node-local throughout, which is the convention the build path already uses (`clade_faith_pd` adds a node's own branch where the node is visited): a leaf's own branch goes into the value it returns, and the parent adds only `rk.subtree_pd`. Checked against `clade_faith_pd` on 800 random trees, the patched recursion agrees exactly; the previous parent-local form disagreed on 409 of them. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

The empty-composition case built a four-sample table but compared it against `groups8[1:4]`, which is every sample in group 'A', and it passed `min_prevalence` where the constructor takes it positionally. Both errors were masked by the `erfc` UndefVarError that aborted the testset before this block ran; with that fixed, CI reports the group error instead of the prevalence one. Use all eight samples with a table in which no taxon appears in every sample, so min_prevalence = 1.0 leaves nothing to fit and the engine raises "no composition to model". Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

sonarqubecloud · 2026-10-23T08:25:49Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

…pe widening, and route deduplication Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Main landed #226 while this branch was in review, and the two found three of the same defects independently. Main's resolution is taken for all three, since it is already on main: - `erfc`: main's private `_erfc` replaces the `compositional_erfc` added here. Same algorithm (incomplete gamma at a = 1/2, series below x^2 = 1.5 and a Lentz continued fraction above), so only the name and the tests differ; `compositional.jl` and `test_differential.jl` are taken wholesale from main. - `subtree_pd` in `_reaggregate_after_move`: identical fix, main's `own_pd` naming and one-line post-loop form kept. Git had merged the two variants additively, which would have counted every active internal branch twice; that is resolved to a single addition. - The `Main.SV` collision that was aborting the include loop: main renames this file's binding to `CLADE_SV` instead of dropping `const`. Main's rename is kept. - `min_prevalence` in the multinomial engine test: main's eight-sample table is better than the four-sample one here, and is kept. Kept from this branch, because main does not have them: - The raw like-weight ratio in the diversity block. Main's change to that line only renames `c.weight` to `c.like_weight` and keeps `cand.like_weight / tw`, which is the renormalisation Codex objected to on #223: it hands a lone 0.6 placement a weight of 1.0. The divisor is removed, and the mass the tool never placed is reported as `unplaced_reads`. - `_sample_total` and the `total_a`/`total_b`/`totals` arguments on `weighted_unifrac`, `branch_unifrac_contributions` and `unifrac_matrix`, with the route passing each sample's library size. Without them the metric divides by the placed-only mass and undoes the line above. - Per-file testsets in `runtests.jl`. Main fixed the `SV` collision but not the reason one bad binding could silently skip thirty-five unit files and the occupancy probe. - `_cc_find`, and the drag-and-drop assertions that pin the exact post-move PD values and total-PD conservation rather than comparing a positional index against an inequality.

Main landed #226, which contains equivalents of this branch's _erfc implementation, min_prevalence test fix, edge_number graft fix and stem-inclusive subtree PD, plus #217's validated-statistics implementation and the CLADE_SV rename that removes the Main.SV const collision. Conflicts resolved in favour of main for those; this branch keeps its unique additions: AbstractString tree helpers and the structured clade_cumulus_failed catch-all with the like_weight diversity fixes. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

hyperpolymath and others added 19 commits October 23, 2026 00:15

fix(analysis): restore differential method integrations

eab3a51

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix(ci): check references at their embedded precision

875aac5

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

ci: surface validated-statistics test failures

9f49f53

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Merge remote-tracking branch 'origin/main' into arena/dd990535-metama…

631ec2e

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix: repair DOI module parsing and syntax gate

1079b77

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Merge branch 'main' into arena/dd990535-metamanifold-webui

a5d6976

Merge remote-tracking branch 'origin/main' into arena/dd990535-metama…

bc7c21e

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Merge remote-tracking branch 'origin/main' into arena/dd990535-metama…

b49c676

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix(stats): aggregate DuckDB counts exactly

8bc3b7a

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix(stats): preserve JSON integer token validation

9d66d47

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

test(stats): distinguish zero counts from zero totals

5dad736

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix(cladistics): repair phylogeny and route integration

a412bee

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix(cladistics): align grafting and subtree diversity

d5f8060

Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Update .github/workflows/ci.yml

307c9c6

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>

fix(stats): preserve byte-backed request bodies for integer token val…

1268cb0

…idation

chatgpt-codex-connector Bot reviewed Oct 23, 2026

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hyperpolymath enabled auto-merge (squash) October 23, 2026 07:52

hyperpolymath merged commit 87092cc into main Oct 23, 2026
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hyperpolymath deleted the arena/a8928088-metamanifold-webui branch October 23, 2026 09:01

hyperpolymath added a commit that referenced this pull request Oct 23, 2026

Merge main (#226) and retain unplaced jplace mass accounting, tree ty…

09003a9

…pe widening, and route deduplication Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

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Land #217 (exact DuckDB counts) on main, and fix the Wald tail - #226

Land #217 (exact DuckDB counts) on main, and fix the Wald tail#226
hyperpolymath merged 21 commits into
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hyperpolymath commented Oct 23, 2026

What this is

Conflict resolution (4 files)

Two main-line fixes needed to get the required checks green

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