chore(ci): remove Codecov residue — coverage now local artifact - #13
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- Remove codecov.yml (gone) - Remove badge from README.md - Replace codecov/codecov-action@v6 upload with actions/upload-artifact@v4 local lcov.info - Per user request: codecov is gone, residue removed - No gitar found in repo (grep -i gitar returns 0) — if meant another tool, please clarify
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This was referenced Sep 18, 2026
hyperpolymath
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Sep 18, 2026
…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
hyperpolymath
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Sep 18, 2026
…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
arena-ai-coding-agent Bot
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Sep 27, 2026
…-slice kit (#82) ## Summary Establishes the strategic, technical, and operational roadmap for transitioning contributions from the `hyperpolymath/MetaManifold-WebUI` fork back to upstream maintainer **Joshua Jewell** (`JoshuaJewell/MetaManifold-WebUI`), directly addressing his feedback on upstream PR #13. ### What this PR adds 1. **Maintainer Handoff Ultraplan** (`docs/migration/ULTRAPLAN-MAINTAINER-HANDOFF.md`): - **Retraction of PR #13**: Diagnosis of the 159 merge conflicts (merge base reverted to January root commit `06d85ba` after git-filter-repo dead-asset cleanup) and exact closure command + drafted comment for Joshua. - **Maintainer Profile**: Ground rules respecting veterinary science workflows, microbiome amplicon analysis priorities, and team bandwidth. - **8-Track Taxonomy**: Clear classification across Pipeline Fixes, Biological QC, Benchmarks, Statistics Cluster, Test Organization, React UI, Architectural Hard Calls, and Formal Evidence. - **'Free' vs 'Hard Decision' Trade-Off Matrix**: High-clarity breakdown showing what is safe/additive vs what requires architectural choice (YAML vs KYAML, Estate CI vs simple CI, React vs Stipple, exact math vs canonical R pipeline). - **R-Pipeline Protection & Dual-Track CI/CD**: Guarantees that canonical biological tools (`dada2`, `vegan`, `MASS::glm.nb`) remain the primary blocking ground truth. - **Phased PR Sequencing**: Atomic clean-branch roadmap re-anchored on `ecefb1c` (upstream `main`) with zero conflicts and zero Stipple/Vue dependencies. 2. **Automated Upstream Slicing Kit** (`scripts/prepare-upstream-slices.sh`): - Fetches `upstream/main` (`ecefb1c`). - Generates four atomic, conflict-free branches directly from `ecefb1c` in temporary worktrees: - `upstream-slice/01-qc-and-fixes` (FastQC/MultiQC in CI + 1x1 matrix & zero-depth fixes, 6 files) - `upstream-slice/02-benchmarks` (`bench/` suites, 16 files) - `upstream-slice/03-statistics-cluster` (real models, exact offsets, test renames, 16 files) - `upstream-slice/04-frontend-polish` (accessible dialogs, TS types, 13 files) - Excludes `ui/` and all Genie/Stipple dependencies completely. - Verifies zero merge conflicts against upstream `main`. ### Hygiene & Conformance - `scripts/check-spdx.sh`: OK (361 files covered). - `scripts/check-format.sh`: OK (465 files checked). Co-authored-by: hyperpolymath <6759885+hyperpolymath@users.noreply.github.com> Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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Summary
Removes Codecov for certain per user request.
CI
Should make CI green for codecov removal, no longer requires CODECOV_TOKEN secret.
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