fix(analysis): restore differential method integrations by hyperpolymath · Pull Request #211 · hyperpolymath/MetaManifold-WebUI

hyperpolymath · 2026-10-23T00:15:43Z

Summary

restore all nine differential methods, their complete configuration, dispatch, diagnostics, and HTTP error mappings
repair method-dependent config validation and forwarding, including multinomial optimizer/reference settings
restore the frontend API/config union, method-specific CSV provenance, and both distinct CladeCumulus workflows
reinstate both rational-budget regressions and expand differential route/config coverage

Validation

npm run build (frontend) — passed
bun test src — 85 passed, 0 failed
Julia tests and occupancy validation — running in CI (Julia is unavailable in the local workspace)

This is a focused integration repair; it does not resolve the broader validated-statistics acceptance work in #1.

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

chatgpt-codex-connector · 2026-10-23T00:15:50Z

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coderabbitai · 2026-10-23T00:15:52Z

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Reviewing files that changed from the base of the PR and between c06c0d4 and 875aac5.

📒 Files selected for processing: 14

config/defaults/pipeline.yml
frontend/src/api/types.ts
frontend/src/components/DifferentialPanel.tsx
frontend/src/components/PipelineStages.test.ts
frontend/src/components/PipelineStages.tsx
frontend/src/components/differentialTable.test.ts
frontend/src/components/differentialTable.ts
frontend/src/views/StudyView.tsx
src/analysis/differential.jl
src/server/routes/analysis.jl
src/server/routes/config.jl
test/references/check_high_precision_references.py
test/unit/test_differential.jl
test/unit/test_numeric_policy.jl

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…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>

github-actions · 2026-10-23T00:18:17Z

Fork governance

Lane	Status	Run
DEED syntax (repo deed)	🟢 conformant	run 39877855708
Hypatia verdict grid	purple (job: success)	same run

🟣 critical · commit 875aac52ddef · run 39877855708

Reporter	Status	Critical	High	Medium	Since previous revision
Hypatia scan	🟣 critical	47	63	31	↔ unchanged
panic-attack assail	🔴 high	0	5	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: 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: 18 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 — 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.

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

sonarqubecloud · 2026-10-23T00:24:52Z

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

…s main lost Rebased onto main (c978994, which includes #208/#211/#213) so this is only the part main still gets wrong. Package loading — `using MetaManifold` fails on main: - src/core/doi.jl declared `module DOI` twice (lines 4 and 21) with one terminator, a ParseError at EOF before any test can run. The declaration after the header comment is kept. - src/MetaManifold.jl included analysis/clade_cumulus.jl twice and never included analysis/compositional.jl, which Differential imports CompositionalModels from (UndefVarError as soon as it is loaded). Both corrected in place. - src/server/server.jl never included routes/cladistics.jl, so the study-level Cladistics tab the frontend calls returns 404 while the route file sits unused. Included after clade_cumulus.jl; no path or helper clashes. Test registration: - test/runtests.jl listed test_clade_cumulus.jl twice and had lost test_evidence.jl and test_evidence_routes.jl, which #201 added. 49 files, each once, and every file in test/unit is registered. Statistics tests that contradicted their own sources: - test_exact_summaries.jl expected 0/1 proportions for a zero-read sample, but `_summarise` fills those with `nothing` (a proportion is undefined, not zero, when a sample has no reads) and stores null. Test realigned to the source. - test_high_precision.jl expected UnsupportedRepresentationError for a numeric policy of the wrong mode; `assert_mode` raises ArgumentError for that. Test realigned, with the reason stated inline. Docs main lost in the #196 merge: - docs/statistics/zero-handling.md is back to the full treatment (replacement policies, delta semantics, what the Bayesian posterior does and does not claim, warnings and references) instead of the 60-line summary. - README regains the Evidence Mode section and the differential-abundance method guidance (why a count model rather than a t-test, choosing the reference taxon, overdispersion, which model to use), documents all nine methods and settings, and the config sample lists every differential key. Verified: tree-sitter parses every touched Julia file; no file is included twice; YAML parses with the expected differential keys; `npx tsc --noEmit` clean; `bun test src` 85/85. Julia itself is not available here, so the suite's first real run is CI. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…in lost (#209) Rebased onto `main` (c978994, which now carries #208/#211/#213), so this PR is only the part `main` still gets wrong — and `main` still cannot load the package. ## 1. `using MetaManifold` fails | File | Defect | Effect | |---|---|---| | `src/core/doi.jl` | `module DOI` declared twice (lines 4 and 21) with one terminator | `ParseError` at EOF, before a single test runs | | `src/MetaManifold.jl` | `analysis/clade_cumulus.jl` included twice; `analysis/compositional.jl` never included | module redefined; `UndefVarError: CompositionalModels` when `differential.jl` loads | | `src/server/server.jl` | `routes/cladistics.jl` never included | the Cladistics tab calls endpoints that return 404 while the route file sits unused | Each is a one-line fix in place. `cladistics.jl` is included after `clade_cumulus.jl`; it shares no route path or helper name with the other route files. ## 2. Test registration `test/runtests.jl` listed `test_clade_cumulus.jl` twice and had lost `test_evidence.jl` and `test_evidence_routes.jl`, which #201 added. Now 49 files, each once, and every file in `test/unit` is registered. ## 3. Two statistics tests that contradicted their own sources Both came from a branch whose tests were written against different source behaviour: - `test_exact_summaries.jl` expected `0/1` proportions for a zero-read sample. `_summarise` fills them with `nothing` and stores null, because a proportion is undefined — not zero — when a sample has no reads. The test is realigned to the source; the source is not weakened to the test. - `test_high_precision.jl` expected `UnsupportedRepresentationError` for a policy of the wrong numeric mode. `assert_mode` raises `ArgumentError` for that (a caller error, not an unrepresentable value). Realigned, with the reason stated inline. ## 4. Documentation main lost in the #196 merge - `docs/statistics/zero-handling.md` is back to the full treatment — replacement policies and their exact `cmultRepl` calls, `delta` semantics, what the Bayesian posterior parameterisation does and does **not** claim, warnings, and references — instead of the 60-line summary. - `README.md` regains the Evidence Mode section and the differential-abundance method guidance (why a count model rather than a t-test, choosing the reference taxon, overdispersion, which model to use), documents all nine methods and their settings, and the config sample lists every differential key including the multinomial optimiser budget. ## Validation Julia is not available in my environment, so the Julia side is static: tree-sitter parses every touched file, no file is included twice, every `test/unit` file is registered exactly once, and the YAML parses with the expected differential keys. Frontend: `npx tsc --noEmit` clean, `bun test src` 85/85, `npm run build` succeeds. CI is the first real execution of the Julia suite, and I will follow it and fix what it reports. Co-authored-by: Arena Agent <agent@arena.ai> Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

## Summary - carry the remaining post-#211 Julia validation work on the same branch - publish validated-statistics failure output through Checks annotations, matching the diagnostics already available for the full Julia suite - include the latest main and its independent-reference fixture alignment ## Validation so far - Independent Python Decimal reference check — passed - Frontend build and all 85 frontend tests passed on the integrated tree before the follow-up CI-only change - Full Julia validation is required and will be completed before this PR is considered ready PR #211 was merged externally while its Julia check was failing; this follow-up does not treat that merge as evidence that validation passed. --------- Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…216) ## What is broken on `main` `using MetaManifold` fails on `c978994`, so the Julia suite cannot run at all. Two merge artefacts are left over from the compositional-differential work: | File | Fault | | --- | --- | | `src/core/doi.jl` | `module DOI` declared twice (lines 4 and 21). The inner declaration swallows the module body and leaves the outer one without an `end`, so the file cannot be included. | | `src/MetaManifold.jl` | `analysis/clade_cumulus.jl` included twice, and `analysis/compositional.jl` never included. `Differential` does `using ..CompositionalModels`, so loading dies with `UndefVarError: CompositionalModels not defined`. | The routes (`#211`), the frontend and the unit tests are already correct; this is the remaining piece that keeps the package from loading, plus the documentation the merge dropped. ## Changes - **`src/core/doi.jl`** — remove the duplicated `module DOI`. - **`src/MetaManifold.jl`** — drop the duplicate `clade_cumulus` include; include `analysis/compositional.jl` before `analysis/differential.jl`, with a comment explaining the ordering requirement. - **`README.md`** — restore the `ancom_bc`, `aldex2`, `songbird`, `multinomial` and `dirichlet_multinomial` method bullets, the "why a count model", "choosing the reference taxon" and "overdispersion" sections, and the nine-method `analysis.differential` config block (including `mn_reference_taxon`, `mn_penalty`, `dm_overdispersion_method`, `max_iter`, `tolerance`, `max_seconds`). - **`ROADMAP.md`**, **`docs/statistics/zero-handling.md`** — describe the five compositional models and note that the multinomial models replace no zero. `songbird` (R) and `multinomial` (Julia) remain two implementations of the same baseline-category model, both selectable, neither an alias — as documented in `src/analysis/differential.jl`. ## Verification - `./node_modules/.bin/tsc --noEmit -p .` — 0 errors. - `bun test src` — 85 pass / 0 fail. - `tree-sitter-julia` parse of every `src/**/*.jl` and `test/**/*.jl` — clean (same three known parser false positives as before). - Cross-reference audit: every `Differential.x` / `CompositionalModels.x` reference resolves. - Julia itself is not available in the working environment, so `test/runtests.jl` runs here in CI for the first time since the merge. ## Known, out of scope `src/server/routes/cladistics.jl` is not included by `src/server/server.jl`, and it calls `CladeCumulus.asv_tip_name` / `CladeCumulus.analyse_phylogeny`, which do not exist. Wiring it in as-is would break the server, so it is left untouched; the Cladistics build API needs a follow-up. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

fix(analysis): restore differential method integrations

eab3a51

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

hyperpolymath enabled auto-merge (squash) October 23, 2026 00:17

fix(ci): check references at their embedded precision

875aac5

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

hyperpolymath disabled auto-merge October 23, 2026 00:24

hyperpolymath merged commit 10a4a36 into main Oct 23, 2026
18 of 19 checks passed

hyperpolymath deleted the arena/dd990535-metamanifold-webui branch October 23, 2026 00:24

This was referenced Oct 23, 2026

fix: load the package, and restore the docs and test registrations main lost #209

Merged

ci: surface and resolve remaining Julia test failures #215

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This was referenced Oct 23, 2026

fix(stats): aggregate DuckDB counts exactly #217

Open

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

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fix(analysis): restore differential method integrations - #211

fix(analysis): restore differential method integrations#211
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