fix(core): load the compositional models and unbreak the build tree by hyperpolymath · Pull Request #216 · hyperpolymath/MetaManifold-WebUI

hyperpolymath · 2026-10-23T00:32:50Z

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.

chatgpt-codex-connector · 2026-10-23T00:32:55Z

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github-actions · 2026-10-23T00:34:03Z

Fork governance

Lane	Status	Run
DEED syntax (repo deed)	🟢 conformant	run 39880294701
Hypatia verdict grid	purple (job: success)	same run

🟣 critical · commit a840c5e65a3c · run 39880294701

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.

… handling `ROADMAP.md` still said that `nb_glm` and `clr_welch` "remain the existing differential methods", which stopped being true when `zinb`, `hurdle_nb`, `ancom_bc`, `aldex2`, `songbird`, `multinomial` and `dirichlet_multinomial` landed. It now lists all nine and points at the README section, and records that `songbird` (R) and `multinomial` (Julia) are two implementations of one baseline-category model rather than two models. The zero-handling note explained why a negative-binomial likelihood needs no replacement but said nothing about the two joint multinomial models, whose "when not to replace zeros" advice now names them: a zero count is part of the likelihood, no size factor is fitted, and conditioning on each sample's read total makes every effect a log ratio against a reference taxon. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

sonarqubecloud · 2026-10-23T00:48:55Z

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

#220) Removes the React Evidence surface and keeps the Evidence API, per the owner's ruling on #7: the semantics belong to the theory track, and the browser implementation is being rewritten for the Vue/Marid client, so the React one should not sit in the tree in the meantime. ## What goes | Path | Lines | | --- | --- | | `frontend/src/evidence/` (10 files) | 2401 | | `frontend/src/components/EvidenceModeToggle.tsx` | 21 | | `api.evidence` namespace in `frontend/src/api/client.ts` | 31 | | `evidence` tab in `RunView.tsx` | — | ## What stays `src/core/evidence.jl`, `src/server/routes/evidence.jl`, `test/unit/test_evidence.jl`, `test/unit/test_evidence_routes.jl`. The claim schema (scope 1–50 values ≤200 chars, text ≤2000, ≤5 warrants, ≤20 caveats, blank status → `draft`, `supported` requires ≥1 of measurement/citation/inference), the echo verdicts, containment labels and residual arithmetic are untouched and still covered by the Julia suite. ## Side effect on #7's actual complaint `EvidenceModeToggle` gated the placement `CladeCumulusPanel` in the Trees view — "Evidence Mode currently gates Advanced and CladeCumulus". With the toggle gone that panel renders unconditionally, so the gating the issue describes no longer exists. ## Contract for the Marid client The README `### Evidence Mode (API)` section now documents the endpoints and the server-enforced validation rules instead of the three removed views. ## Verification - `tsc --noEmit -p .` — clean - 10 remaining frontend test files — 169 assertions, 0 failures - `vite build` — succeeds The deleted `evidence.test.ts` covered the UI claim helpers; the rules it mirrored stay tested on the server. This branch is also rebased onto current `main`, and replaces #212 (closed as superseded — every repair it carried landed on `main` via #208–#216). Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

hyperpolymath force-pushed the arena/0ff97d53-metamanifold-webui branch from b1022be to a840c5e Compare October 23, 2026 00:48

hyperpolymath merged commit 7bb716d into main Oct 23, 2026
16 checks passed

hyperpolymath deleted the arena/0ff97d53-metamanifold-webui branch October 23, 2026 00:48

This was referenced Oct 23, 2026

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

Closed

refactor(frontend): remove the Evidence UI, keep the Evidence API (#7) #220

Merged

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fix(core): load the compositional models and unbreak the build tree - #216

fix(core): load the compositional models and unbreak the build tree#216
hyperpolymath merged 1 commit into
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hyperpolymath commented Oct 23, 2026

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hyperpolymath commented Oct 23, 2026

What is broken on main

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