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fix: restore what the last four squash merges overwrote (main is red) - #212
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PRs #204, #206, #196 and #201 each rebased onto an older main and were then squashed onto a newer one, so each squash silently reverted part of the PR before it. main does not build: the frontend typecheck fails 26 times, and src/analysis/differential.jl lost two of its three method families. Restored, per file, from the commit each feature actually landed in: - src/analysis/differential.jl: the ANCOM-BC / ALDEx2 / Songbird dispatch (#206) and the multinomial / Dirichlet-multinomial dispatch (#204), both deleted by #196. METHODS is the union of all nine implemented methods. The two-part NB branch (#196) is untouched. - src/core/doi.jl: `module DOI` was declared twice, leaving an unbalanced end. - src/MetaManifold.jl: analysis/clade_cumulus.jl was included twice, and analysis/compositional.jl was never included although Differential uses it. - test/runtests.jl: the clade_cumulus unit file was registered twice and the two evidence files (#201) had lost their registration, so CI never ran them. - frontend: StudyView imported CladeCumulusPanel from two paths; api/client.ts used three Cladistics types it never imported; differentialTable.configLine lost its per-method cases; PipelineStages offered four of the nine methods. Two tests also asserted contradictory method lists; both now assert the union. - README.md and config/defaults/pipeline.yml: restored the Evidence Mode section (#201) and the per-method documentation (#204, #206). Verified here: tsc --noEmit clean, vite build succeeds, all 11 frontend test files pass (238 assertions), every touched Julia file parses. The Julia suite still has to run in CI — this commit does not claim it passes. Refs #7. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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Superseded by work that landed on Every repair in this branch now exists on
Verified on Merging this branch would now revert newer Remaining |
Pull request was closed
#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>
Why
mainis red, and not from a single mistake. Four PRs (#204 multinomial, #206ANCOM-BC/ALDEx2/Songbird, #196 two-part NB, #201 Evidence Mode) were each
squashed onto a main that had moved on, and each squash reverted part of the PR
merged before it. The result:
bun run build→tsc && vite buildfails with 26 type errors.src/analysis/differential.jlis missing two of its three method families.src/core/doi.jldeclaresmodule DOItwice, so it cannot load at all.src/MetaManifold.jlincludesclade_cumulus.jltwice and never includesanalysis/compositional.jl, whichDifferentialimports from.This PR restores the union, per file, from the commit each feature actually
landed in — I did not re-implement anything that merely went missing.
What was restored
src/analysis/differential.jlMETHODSis now the union of the nine implemented methods.src/core/doi.jlmodule DOIand the unbalancedendsrc/MetaManifold.jlclade_cumulus.jlinclude;analysis/compositional.jlincluded beforeDifferential, which imports ittest/runtests.jltest_clade_cumulus.jl; re-registeredtest_evidence.jlandtest_evidence_routes.jl, which were in the tree but never runfrontend/src/views/StudyView.tsxCladeCumulusPanelimported from two paths (aliased the study-level one)frontend/src/api/client.tsCladistics*types used but never importedfrontend/src/components/differentialTable.tsconfigLinecases, and the Bayesian-onlybayesian_alphaguardfrontend/src/components/PipelineStages.tsxfrontend/src/api/types.tsDifferentialMethodunion,mn_*/max_iter/tolerance/max_secondsconfig fields,diagnostics.modelREADME.md,config/defaults/pipeline.ymlTwo tests asserted contradictory method lists — one demanded four methods,
one demanded five different ones, for the same config key. Both now assert the
union, which is what the backend actually accepts.
Verification
npx tsc --noEmit -p .— clean (was 26 errors).npx vite build— succeeds.file that could not typecheck).
registrations or
UNIT_FILESentries remain anywhere in the tree.The Julia suite has not been run here — there is no Julia or R in this
environment. That is the one thing still to confirm, and CI is where it has to
happen. Two areas are most likely to need a follow-up: the numeric expectations
in
test_evidence*.jl(written without a Julia interpreter) and the R-backedmethod branches, which need R packages installed.
Refs #7.