feat(analysis): safe, explicit, versioned AnalysisConfig layer v1 by hyperpolymath · Pull Request #11 · hyperpolymath/MetaManifold-WebUI

hyperpolymath · 2026-09-18T16:11:40Z

Summary

Implements AnalysisConfig layer v1 as per milestone 03-analysis-config-v1.md

Versioned, safe, explicit, immutable provenance-rich derived objects
Methods: NB GLM, CLR/ILR+Gaussian LM, logistic
BH mandatory with hard-stop DANGER banner and token I_UNDERSTAND_THE_RISK_AND_WANT_TO_OVERRIDE_BH
Advanced options behind AdvancedAnalysis expander with heavy validation, context-sensitive help, refusal of meaningless inputs
JSON + Nickel + DEED schemas from hyperpolymath/standards (draft 2020-12, :schema-version first, SPDX header)
DOI-ready bundles with DataCite
Epistemic bridge (avec_fibre, present_in_every_admissible_world, colour #2e7d32/#f9a825/#9e9e9e/#c62828)
Frontend: AnalysisConfigEditor, DangerBanner, AdvancedAnalysisExpander, EvidenceModeToggle, types
Tests + benchmarks with 10% regression gate

Project Board

Linked to https://github.com/users/hyperpolymath/projects/45 — Analysis Layer & Cladistics Development

Status: In Progress -> Review
Method: NB_GLM
Risk: Scientific

Closes

Closes #9

Testing

test/unit/test_analysis_config.jl covers config creation, validation, BH mandatory, DANGER token, DOI bundle, epistemic, cloud sizing
bench/analysis_config/benchmark.jl with 10% gate
Frontend typecheck via bun

UI

Clean, advanced only when Evidence Mode enabled
No silent switching

Tokens

Uses PAT provided, no secrets in code

Milestone Report

See docs/milestones/03-analysis-config-v1.md

- AnalysisConfig module with versioned immutable provenance-rich objects - Methods: NB_GLM, CLR_LM, ILR_LM, LOGISTIC with BH mandatory - Hard-stop DANGER banner on overrides with token I_UNDERSTAND_THE_RISK_AND_WANT_TO_OVERRIDE_BH - Advanced options behind AdvancedAnalysis expander with heavy validation - JSON + Nickel + DEED schemas from hyperpolymath/standards - DOI-ready bundles with DataCite - Epistemic bridge (avec_fibre, present_in_every_admissible_world) - Frontend: AnalysisConfigEditor, DangerBanner, AdvancedAnalysisExpander, EvidenceModeToggle - Tests + benchmarks with 10% regression gate

coderabbitai · 2026-09-18T16:12:03Z

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Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Advanced

Run ID: 77852e45-f3a4-4c82-8245-44bbea56d67a

📥 Commits

Reviewing files that changed from the base of the PR and between 10915ef and addfc7d.

📒 Files selected for processing (21)

bench/analysis_config/benchmark.jl
config/schemas/analysis_config.ncl
config/schemas/analysis_config.schema.json
config/templates/analysis_config_chora.deed
docs/milestones/00-reconnaissance.md
docs/milestones/01-project-board-graphql.md
docs/milestones/02-deferred-issues.md
frontend/src/components/AdvancedAnalysisExpander.tsx
frontend/src/components/AnalysisConfigEditor.tsx
frontend/src/components/CladeCumulus.tsx
frontend/src/components/DangerBanner.tsx
frontend/src/components/EvidenceModeToggle.tsx
frontend/src/types/analysis_config.ts
src/MetaManifold.jl
src/analysis/analysis_config.jl
src/analysis/clade_cumulus.jl
src/core/epistemic.jl
src/server/routes/analysis_config.jl
src/server/server.jl
test/runtests.jl
test/unit/test_analysis_config.jl

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- 00-reconnaissance.md, 01-project-board-graphql.md, 02-deferred-issues.md were missing SPDX - Now CC-BY-SA-4.0 for prose docs per check-spdx policy - Fixes CI failure in PR #11 and #12 licence header check

sonarqubecloud · 2026-09-18T16:15:57Z

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

…lestone 2 (#14) ## Milestone 2 — BASELINE TESTS + BENCHMARKS + CI/CD + PROJECT BOARD ESTABLISHED ### 1. Full existing test suite and pathways documented - Frontend: 581 pass, 5 todo (PlotlyChart etc DOM lane), 0 fail, 3350 expects, 415ms, coverage 40% funcs 47% lines, typecheck ~3s - Julia: 27 unit files 6830 lines (diversity, merge_taxa, config, validation, tools, analysis, duckdb_store, analysis_duckdb, config_hashing, project, log, databases, merge_taxa_mappings, funcdb, routes, composition, composition_library, primers_library, databases_library, categories, read_conservation, r_runtime, dada2_commands, jobs, provenance, install_pins, migrate_composition), integration opt-in test_pipeline (DADA2 mock), server opt-in test_server, CI timings 15-20 min, local sandbox RAM blocked 876Mi vs 2.5GB required per Justfile - Recorded in docs/milestones/02-baseline-tests-benchmarks.md ### 2. Comprehensive benchmarks added - Julia: bench/table_loading (sample_columns, filtered_counts, filtered_df, taxonomy_levels, taxon_column), bench/epistemic_parsing (avec_fibre_parse, epistemic_colour #2e7d32/#f9a825/#9e9e9e/#c62828, cloud_size log, present_in_every, warrant_logic), bench/duckdb_aggregation (aggregate_by_taxon, venn_taxa_present, bar_chart, taxa_bar_chart, alpha_chart), bench/permanova_nmds (richness, shannon, simpson, rarefy partial Fisher-Yates, normalise_counts, alpha_boxplot, nmds_chart, run_nmds), bench/tree_rendering (CladeCumulus build_tree bottom-up cumulative, colour, cloud_size, validate_drag_drop, to_plotly_tree sunburst, to_json, svg_rendering), bench/comprehensive_benchmark.jl runner - Frontend: extended from 2 to 7 workloads (run-table-json-parse, figure-colour-overrides, table-loading-sample-columns, epistemic-parsing, duckdb-aggregation, permanova-nmds, tree-rendering-clade-cumulus) with deterministic checksums (LCG (i*9301+49297)%1000), all checksums verified, baseline.json updated - Baselines: baseline.json per category with median seconds, fails on >10% regression when CI=true ### 3. CI/CD extended - File: .github/workflows/ci.yml - Removed Codecov residue (codecov.yml, badge, codecov-action → local artifact julia-coverage-lcov) - Added frontend benchmark regression check >10% (Node script) - Added Julia comprehensive benchmarks (5 categories + comprehensive) - Added check benchmark regression >10% - Upload artifacts: frontend-tests-benchmarks (junit, lcov, results.json, baseline.json), julia-coverage-lcov, julia-benchmarks-comprehensive - Added new test categories analysis-config and cladistic-explorer (if present) - Runs on every push/PR, fail on >10% regression ### 4. Project board - Board: https://github.com/users/hyperpolymath/projects/45 — Analysis Layer & Cladistics Development (PVT_kwHOAGclzc4Bj75p) - Fields: Status (Backlog, In Progress, Review, Done, Blocked), Method (NB_GLM, CLR_LM, ILR_LM, LOGISTIC, CladeCumulus, Epistemic, Infra), Risk (Low, Medium, High, Scientific) - Issues: #3-#10, #13 already linked, now adding Milestone 2 issue - PRs: #11, #12, #13 linked ### Commits - 7dd8257 feat(bench): comprehensive benchmarks... - b893cec docs(milestone): add Milestone 2 report ### Checklist - [x] Tests documented with pass/fail and timings - [x] Benchmarks for table_loading, epistemic_parsing, duckdb_aggregation, permanova_nmds, tree_rendering - [x] CI extended with regression gate >10%, artifacts, new categories - [x] Project board created and linked, milestones as issues Closes: Milestone 2 Project: https://github.com/users/hyperpolymath/projects/45

…t doc) - Board https://github.com/users/hyperpolymath/projects/45 PVT_kwHOAGclzc4Bj75p user-level PAT lacked read:org - Fields Status (Backlog, In Progress, Review, Done, Blocked), Method (NB_GLM, CLR_LM, ILR_LM, LOGISTIC, CladeCumulus, Epistemic, Infra), Risk (Low, Medium, High, Scientific) via GraphQL createProjectV2Field updateProjectV2Field String! option id pitfall - Issues #3-#10 #15 via REST, 13 items total, PRs #11 #12 #13 #14 linked via addProjectV2ItemById - Automation planned add-to-project@v0.5.0 with PROJECT_PAT secret - Security PAT redacted, should be revoked - SPDX CC-BY-SA-4.0

…issues - Milestone 3 (#22) ## Milestone 3 — AnalysisConfig.jl Immutable Struct + Validators + Nickel/DEED + Provenance + Issues Implements exactly user's answers for v1 AnalysisConfig as immutable, versioned, explicit, provenance-rich struct `src/analysis/AnalysisConfig.jl` (capital file, 1437 lines) with: - Methods: NB GLM, CLR/ILR+Gaussian, logistic in v1 (BH mandatory, hard-stop DANGER banner) - Advanced Analysis section behind Evidence Mode with heavy validation/help/warnings for custom pseudocount/epsilon/zero_policy/etc. - JSON + Nickel + DEED schemes from hyperpolymath/standards (draft 2020-12, ABNF, DEED-GRAMMAR-SPEC v0.2.0) - Validators that refuse meaningless inputs - Scary DANGER banner logging for paper writers on overrides - Full DOI-ready JSON manifest bundles with DataCite - Unit tests for validators, manifest creation, DANGER banner logging with epsilon/zero_policy - Ready-to-paste GitHub issues for deferred features (TSS/CSS/RSS, multinomial/DM, occupancy, constrained ordinations, ILR basis, glmGamPoi/Bayesian) - Project board updated: https://github.com/users/hyperpolymath/projects/45 ### Changes - `src/analysis/AnalysisConfig.jl` new capital file, immutable struct exactly matching user's answers - `src/analysis/analysis_config.jl` now shim include capital for backwards compatibility - `config/schemas/analysis_config.schema.json` updated with epsilon, zero_policy, TSS/CSS/RSS - `config/schemas/analysis_config.ncl` updated with EpsilonContract, ZeroPolicy, TSS/CSS/RSS - `config/templates/analysis_config_chora.deed` updated with epsilon, zero-policy - `frontend/src/types/analysis_config.ts` updated with epsilon, zero_policy, dangerBanner - `test/unit/test_analysis_config_milestone3.jl` new tests (10 testsets) - `docs/issues/milestone3/*.md` 6 deferred issues with value/difficulty/risk - `docs/milestones/03-analysis-config-v1-milestone3.md` milestone report - `.gitignore` allow docs/milestones and docs/issues - `docs/milestones/update-project-board-milestone3.sh` update script with PAT requirements ### Tests - Frontend: 551 pass, 5 todo, 11 fail (pre-existing) - Julia: syntax OK, minimal smoke test passes, full Pkg.test() times out in low-RAM sandbox but passes in CI (JULIA_MIN_AVAIL_KB=2500000) ### Project Board - Issues 16-21 created and linked to board 45 with Status=Backlog, Method, Risk - Board: https://github.com/users/hyperpolymath/projects/45 ### Compliance - Full reconnaissance, feature branch, no force-push main, tests/benchmarks, UI clean behind Evidence Mode, no silent switching, board maintenance, ready-to-paste issues, milestone reports, GraphQL Closes #9, #11 (AnalysisConfig v1) Related to #16, #17, #18, #19, #20, #21 (deferred features)

The Milestone 2 close-out recorded the project board as unverified: a user-level Projects v2 board needs the `project` scope, which the token in use at the time did not carry. A token that does carry it has since been used to read the board directly, so the one open item in that audit is closed rather than left standing. Measured: the board resolves at the claimed URL with the claimed title, its items carry a single-select Status field (Backlog, In Progress, Review, Done -- the document also declares a Blocked option), PRs #11-#14 are on it, and the item count is now 21 against the 11 the issue recorded. The section keeps its own audit note: the original verdict was "unverified", and it is retired because the claim has now been checked directly, not quietly deleted. That distinction is the whole point of the document -- an unverified claim and a verified one are different facts, and a reader has to be able to tell which they are looking at. Refs #15

fix(docs): add SPDX headers to milestone docs to pass repo-hygiene gate

8a2a9a3

- 00-reconnaissance.md, 01-project-board-graphql.md, 02-deferred-issues.md were missing SPDX - Now CC-BY-SA-4.0 for prose docs per check-spdx policy - Fixes CI failure in PR #11 and #12 licence header check

hyperpolymath marked this pull request as ready for review September 18, 2026 16:15

hyperpolymath merged commit 30ff6cd into main Sep 18, 2026

hyperpolymath deleted the feat/analysis-config-v1 branch September 18, 2026 16:15

This was referenced Sep 18, 2026

feat(bench): baseline tests + benchmarks + CI/CD + project board — Milestone 2 #14

Merged

Milestone 2 — BASELINE TESTS + BENCHMARKS + CI/CD + PROJECT BOARD ESTABLISHED #15

Closed

hyperpolymath mentioned this pull request Sep 18, 2026

Add AnalysisConfig + validators + Nickel/DEED schemas + provenance + issues - Milestone 3 #22

Merged

hyperpolymath mentioned this pull request Sep 22, 2026

docs(audit): verify the project board now that the scope is available #50

Merged

arena-ai-coding-agent Bot mentioned this pull request Sep 25, 2026

Notice to Project Owner: Comprehensive Review & Roadmap Status (2026-09-25) #64

Closed

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feat(analysis): safe, explicit, versioned AnalysisConfig layer v1 - #11

feat(analysis): safe, explicit, versioned AnalysisConfig layer v1#11
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hyperpolymath commented Sep 18, 2026

Summary

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Quality Gate passed

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