Null-calibration bench + small-sample caveat (#193), with cross-PR integration repair by hyperpolymath · Pull Request #214 · hyperpolymath/MetaManifold-WebUI

hyperpolymath · 2026-10-23T00:29:08Z

Why

This branch carries the fork-side resolution of #193 and, because the squash merges of #196–#207 left main unable to build the frontend or load the Julia package, the integration repair needed to land anything at all. A file-by-file audit (every squash commit matched its PR-head tree exactly) traced the breakage to PR-branch conflict resolutions overwriting each other:

feat(cladistics): add CladeCumulus ASV phylogenies #200 dropped include("analysis/compositional.jl") while differential.jl requires ..CompositionalModels.
feat(cladistics): CladeCumulus phylogenetic & epistemic integration #207 duplicated the clade-cumulus include/panel import, dropped the cladistics client imports, and replaced routes/cladistics.jl with routes/clade_cumulus.jl.
feat(analysis): Advanced compositional methods — ANCOM-BC, ALDEx2, Songbird #206 then feat(analysis): add two-part count models and occupancy fitter #196 overwrote the differential method/config union: DifferentialConfig referenced undefined mn_*/dm_*/max_* names, the ancom_bc/aldex2/songbird and multinomial dispatch branches were unreachable, and _differential_settings_error called an undefined keys_.

What

#193 (ad7f5f2): bench/null_calibration/ extracts the production NB R block and measures Wald/LRT null rejection (WebR + genuine MASS 7.3-65 reduced run executed; full grid + wald_trend/glmGamPoi QL/edgeR committed unrun — REPORT.md bounds exactly what ran). nb_glm results carry diagnostics.calibration_caveat (every ml result, scaled by the smaller group; glmGamPoi through 12/group), surfaced in the panel and CSV header. No p-value or default changes.

Merge (no-ff, by request): current main merged in; conflicts resolved onto main-side structure with the #193 changes reapplied.

Integration repair (1335ccd): nine-method registry/config/dispatch union, compositional + cladistics/clade-cumulus routes restored, frontend type/config/CSV unions, panel import disambiguated, stale test pins updated to the union.

Verification

Frontend: tsc clean, bun test 87/87, production build passes.
Julia: no runtime in the authoring sandbox — CI is the evidence; this PR stays open until it is green.

Refs #193 (fork-side bench + warning per maintainer decision; upstream default remains the upstream maintainer's call — draft in bench/null_calibration/UPSTREAM_DRAFT.md).

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

…nifold-webui # Conflicts: # README.md # config/defaults/pipeline.yml # frontend/src/api/types.ts # frontend/src/components/PipelineStages.tsx # frontend/src/components/differentialTable.ts # src/analysis/differential.jl Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

The squash merges of #196-#207 left main unable to build: PR-branch conflict resolutions overwrote each other's differential method registry, dropped the compositional include and cladistics routes, duplicated the clade-cumulus include and frontend panel import, and corrupted _differential_settings_error. - MetaManifold.jl: restore analysis/compositional.jl, include clade_cumulus.jl once; server.jl includes routes/cladistics.jl and routes/clade_cumulus.jl. - differential.jl: rebuild the 9-method registry and DifferentialConfig union (mn/dm optimiser + mc_samples), restore ancom_bc/aldex2/ songbird and multinomial dispatch branches alongside the two-part models; routes build the union config; config validation regains the mn/dm cross-key rules. - Frontend: union DifferentialMethod/config/diagnostics types, restore cladistics client imports, alias the cladistics panel so it no longer collides with the clade-cumulus panel, restore per-method CSV config lines and PipelineStages entries for all nine methods. - Tests that pinned pre-union method lists and the 11-column CSV are updated to the union reality. Frontend: tsc clean, bun test 87/87, production build passes. Julia: exercised by CI (no Julia runtime in the authoring sandbox). Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

chatgpt-codex-connector · 2026-10-23T00:29:14Z

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coderabbitai · 2026-10-23T00:29:21Z

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Reviewing files that changed from the base of the PR and between 8a37159 and b7539f9.

⛔ Files ignored due to path filters: 3

bench/null_calibration/results/calibration_summary.csv is excluded by !**/*.csv
bench/null_calibration/results/power_summary.csv is excluded by !**/*.csv
bench/null_calibration/results/provenance_summary.csv is excluded by !**/*.csv

📒 Files selected for processing: 17

README.md
bench/null_calibration/.gitignore
bench/null_calibration/README.md
bench/null_calibration/REPORT.md
bench/null_calibration/UPSTREAM_DRAFT.md
bench/null_calibration/calibration.R
bench/null_calibration/summarise.R
bench/null_calibration/webr_run.mjs
config/defaults/pipeline.yml
frontend/src/api/types.ts
frontend/src/components/DifferentialPanel.tsx
frontend/src/components/PipelineStages.tsx
frontend/src/components/differentialTable.test.ts
frontend/src/components/differentialTable.ts
src/analysis/differential.jl
src/server/server.jl
test/unit/test_differential.jl

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…nifold-webui # Conflicts: # config/defaults/pipeline.yml # frontend/src/api/types.ts # frontend/src/components/PipelineStages.test.ts # frontend/src/components/PipelineStages.tsx # frontend/src/components/differentialTable.ts # frontend/src/views/StudyView.tsx # src/analysis/differential.jl # src/server/routes/analysis.jl # test/unit/test_differential.jl Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

github-actions · 2026-10-23T00:33:39Z

Fork governance

Lane	Status	Run
DEED syntax (repo deed)	🟢 conformant	run 39880010320
Hypatia verdict grid	purple (job: success)	same run

🟣 critical · commit b7539f90ae3a · run 39880010320

Reporter	Status	Critical	High	Medium	Since previous revision
Hypatia scan	🟣 critical	47	63	31	↔ unchanged
panic-attack assail	🔴 high	0	6	13	↓ regressed (1 more blocking)
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: 141 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
121 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 3 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.

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

sonarqubecloud · 2026-10-23T00:46:46Z

Quality Gate passed

Issues
33 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
2.9% Duplication on New Code

See analysis details on SonarQube Cloud

…ion) (#218) Follow-up to #214: `main` CI still fails at 'Run validated-statistics tests first'. **Root cause** (reproduced against DuckDB locally): `_validated_duckdb_counts` selected bare count columns beside `GROUP BY <feature>`: ``` Binder Error: column "s1" must appear in the GROUP BY clause or must be part of an aggregate function ``` so `POST /api/v1/studies/{study}/runs/{run}/statistics/summaries` returned 500 and `test_validated_statistics.jl:180` failed on every branch. **Fix:** fetch rows `ORDER BY feature` and sum rows sharing a feature in Julia `BigInt`. Aggregating in SQL is not an option: `SUM` over HUGEINT counts overflows exactly the values this path exists to keep exact (the test sums 2^126 + 2^126). Per-cell missing/negative/non-integer validation is unchanged; the cell budget is now checked on aggregated features. Julia evidence is CI on this PR (no Julia runtime in the authoring sandbox; the SQL failure itself was reproduced with Python duckdb 2.0.0). --------- Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…ute loading (#222) Follow-up to #214/#218. With the frontend, differential and validated-statistics suites green, the Julia suite stands at 817 pass / 3 fail / 14 error — every remaining failure inside the CladeCumulus testset from #207, masked until now by the broken build. - `_graft_jplace_queries` read `QueryCandidate.weight/.distal_length/.pendant_length`; the fields are `like_weight/distal_len/pendant_len` (FieldError on any valid graft). - `PLACEMENT_WEIGHT_SUM_TOL = 1e-5` marked a single retained placement at LWR 0.98 undecided; truncated candidate lists legitimately sum to slightly less than 1, so tolerance is 0.05 (0.40 still undecided). - The Newick label reader consumed `[&&NHX:B=92]` after `)` without capturing it; capture refs are threaded through `read_label_and_quoted`. - The sources route enumerated views via `SHOW TABLES` and then could not bind a session-registered DataFrame view on a fresh connection (500); it now uses `duckdb_tables()`. - `_load_run_table_df` rejected JSON3 `SubString` table names; arguments normalise to `String` at the boundary. - The FastTree mock in tests addressed `PH.Tools`, but `Phylogeny` imports only selected names from `Tools`; it now addresses `MetaManifold.Tools`. Julia evidence is CI on this PR (no Julia runtime in the authoring sandbox). --------- Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

hyperpolymath and others added 3 commits October 23, 2026 00:13

bench(differential): null-calibration bench + small-sample caveat (refs

ad7f5f2

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

Merge remote-tracking branch 'origin/main' into arena/dc1d6938-metama…

b7539f9

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

hyperpolymath merged commit 50a0e7f into main Oct 23, 2026
13 of 14 checks passed

hyperpolymath deleted the arena/dc1d6938-metamanifold-webui branch October 23, 2026 00:45

This was referenced Oct 23, 2026

fix: restore what the last four squash merges overwrote (main is red) #212

Closed

Fix validated-statistics run summaries 500 (invalid GROUP BY aggregation) #218

Merged

hyperpolymath mentioned this pull request Oct 23, 2026

Fix CladeCumulus testset: field names, NHX capture, LWR tolerance, route loading #222

Merged

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Null-calibration bench + small-sample caveat (#193), with cross-PR integration repair - #214

Null-calibration bench + small-sample caveat (#193), with cross-PR integration repair#214
hyperpolymath merged 5 commits into
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