feat(cladistics): CladeCumulus cumulative explorer with epistemic colours and drag-drop - #12
Merged
Merged
Conversation
|
Warning Review limit reachedNext included review available in 56 minutes. View limit detailsLimit details: You’ve used the included review currently available. You've used all free OSS reviews for now. Wait for the free limit to reset to keep reviewing this public repository. Review configuration: ⚙️ Run configurationConfiguration used: Organization UI Review profile: ASSERTIVE Plan: Advanced Run ID: 📒 Files selected for processing (2)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
hyperpolymath
marked this pull request as ready for review
September 18, 2026 16:15
hyperpolymath
force-pushed
the
feat/clade-cumulus
branch
from
September 18, 2026 16:15
099cff3 to
a6e50e6
Compare
|
This was referenced Sep 18, 2026
hyperpolymath
added a commit
that referenced
this pull request
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
added a commit
that referenced
this pull request
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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Implements CladeCumulus — Cumulative Cladistic Explorer
Project Board
Linked to https://github.com/users/hyperpolymath/projects/45
Closes
Closes #10
Dependencies
Testing
UI