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Arena/01a0db23 metamanifold webui - #97
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Pilot ruling of 2026-09-26 (owner): this repository is the pilot for migrating the estate's YAML to KYAML, the strict YAML subset of KEP-5295. Authority is hyperpolymath/standards 3-practice/YAML-POLICY.adoc rules Y-2 and Y-3. - scripts/kyaml/KYAML.jl: the switch. --to-kyaml, --to-yaml, --check and --report; comments keep their association; canonical-form checking makes the gate idempotent by construction; a refusal names the file and line and writes nothing, so a tree is never half-converted. - config/kyaml/drift.txt: the two workflow files Dependabot and gh actions-lock rewrite. Converted, not gated, accepted in writing (policy §5 step 6). - Justfile: use-kyaml, use-yaml, check-kyaml (wired into hygiene and ci), kyaml-report, and prove-agda, which fails loudly when no Agda is on PATH. - docs/pilots/kyaml-pilot.md: the operating manual — the ruling, what the switch guarantees, what it refuses by name, the decisions it takes and prints, the proof-obligation table, how to revert, and what is deliberately out of scope. - test/unit/test_kyaml.jl: comment association, idempotence, YAML round trip, block scalars, the forced decisions, six refusals, a dropped-comment mutant that must turn the gate red, and every tracked YAML file parsed and re-emitted. - EXPLAINME.adoc: the language ruling (Julia for everything we can; the dada2 pipeline stays as it is; the TypeScript view is a plan, not a task) and the KYAML pilot pointer. - proofs/agda/README.md: how to run the proofs, what each proves, what is deliberately not proved, and what would falsify them. *.agdai ignored. Not in this commit: the conversion itself (next), the shell extraction out of ci.yml into scripts/ci/*.sh, the CI step for check-kyaml, and the Agda CI job. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
…ort (issue #21) Zero handling, implemented rather than aliased, and proved where it can be proved. Operators (src/analysis/zero_replacement.jl): - multiplicative replacement (Martin-Fernandez et al. 2003), the operator of zCompositions::multRepl: zeros get delta x per-part detection limit, observed parts scale by 1 - Delta, and the sample total and the ratios among observed parts are preserved exactly. - Bayesian multiplicative replacement (Martin-Fernandez et al. 2015), the GBM of cmultRepl: posterior mean of a Dirichlet-multinomial with the leave-one-out prior mean and concentration 1/gmean(t) unless alpha is supplied, with the reference's frac x colmins cap and its adjust switch. - Both refuse by name what they cannot do, record per-sample diagnostics, and carry the provenance sentence the issue asks for: all replacement is biased. Dispersion (src/analysis/dispersion.jl): - pure-Julia port of glmGamPoi (Ahlmann-Eltze & Huber 2020): Cox-Reid adjusted NB maximum likelihood with the reference's 0.99 factor and its early returns, the dnorm-weighted local-median trend, the quasi-likelihood conversion, and the inverse-chisquare prior by Nelder-Mead. - The reference's natural-spline abundance trend is NOT ported: true is refused, null is refused at or above 100 features, false runs the reference's own non-trended prior and records the deviation. No silent substitution. - estimation.jl: the by-name refusal becomes the real two-pass path (mean sweep in R, dispersions in Julia, refit at fixed dispersion; theta = 1/alpha, with stats::glm(poisson()) where alpha is 0). Configuration and surface: normalization.bayesian_multiplicative_alpha and advanced.{zero_replacement_method, multiplicative_delta, bayesian_alpha, glmgampoi_abundance_trend} in the Julia model, the Nickel contract, the JSON schema and the frontend types; delta in (0,1) and alpha > 0 validated at the door; warnings below 0.01 and at or above 0.9; a DEED echo of every value; the DANGER banner when three or more deltas have been tried. The Advanced expander gains the delta slider with a replacement preview, the alpha field and the trend selector. Proofs (proofs/agda/, Agda 2.7.0.1 + stdlib 2.1.1, --safe, no postulates): totals and ratios preserved, imputed values positive and below their detection limit; no data-determined rule can be faithful (the fibre behind "every replacement is biased"); the shrinkage lies between the prior and the sample estimate. proofs/agda/README.md states what is not proved and what would falsify each file. Tests and benchmarks: - test/unit/test_zero_replacement.jl and test_dispersion.jl against test/fixtures/issue21/golden.json, with direct comparisons against zCompositions and glmGamPoi wherever R has them and an explicit "this comparison did not run" where it does not; - bench/zero_replacement/benchmark.jl at 100/1000/10000 taxa with the issue's 5-minute warning and the 10% regression report behind METAMANIFOLD_BENCH_STRICT (the repository's later decision made the other Julia benches informational; the reasoning and the switch are recorded in the file header). KYAML pilot follow-ups in the same change: the KYAML tool now preserves comments that sit above the document root instead of dropping them (every file here starts with an SPDX header, so a silent drop would have deleted licence headers); guix.scm gains the agda + agda-stdlib lane; stapeln.toml and Containerfile define the standalone toolchain deployment (owner ruling: standalone, not local-only); the review bench lane is added to the existing Julia benchmark step. The three new Agda modules are flat, standalone-checked files: folding them into the existing MetaManifold/ suite (module namespace, the suite OPTIONS header, All.agda, a guard run) is the follow-up, and doing it blind would have risked a passing lane. Docs: docs/statistics/zero-handling.md, docs/statistics/method-conditions/dispersion-glmGamPoi.md, CHANGELOG, ROADMAP. Not in this commit: the KYAML conversion itself (one command, where Julia is), the shell extraction from ci.yml into scripts/ci/*.sh, and the first CI run of any of it - the sandbox has no Julia or R, so every number here is unexecuted locally and the first CI run is the debugger. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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I isolated the two Dependabot fixes in targeted PR #98 rather than folding them into this broader branch: #98 When reapplying/rebasing any The full KYAML conversion remains separate; it is not included or claimed complete here. |
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Summary
Base check
hyperpolymath/MetaManifold-WebUI:main(not the upstreamparent; application changes go to
JoshuaJewell/MetaManifold-WebUI)Changes
Engineering checklist
Required
bun run checkpasses (frontend/: typecheck 0 errors, tests,benchmarks)
scripts/check-spdx.sh/check-format.sh/check-lint.shpass(advisory in CI — does not block merge)
CONTRIBUTING.md; advisory in CI)NOTICEexplainsthe authorship rule)
.env, or sequencing data includedAs applicable
CHANGELOG.mdupdated for user/developer-visible changesdocs/types/architecture.mdupdated if type boundaries moveddocs/testing/coverage.mdupdated if test coverage moveddocs/reproducibility.mdupdated if environment requirements changedTesting