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ef893c5
sync: review anticipated upstream baseline and isolate remaining fork…
hyperpolymath Oct 17, 2026
bafa901
proofs: scope significance model as an experimental interface (#183)
hyperpolymath Oct 17, 2026
f151d29
fix(charts): isolate title markup stripping (#179)
hyperpolymath Oct 17, 2026
abf6f0d
feat(occupancy): isolate memory grading and proof integration (#184)
hyperpolymath Oct 17, 2026
a843a83
fix(server): isolate wildcard IP origins and reject overflowing ports…
hyperpolymath Oct 17, 2026
00c3613
feat(canonical): isolate JSON canonicalization utility (#182)
hyperpolymath Oct 17, 2026
a84b24f
feat(differential): add reproducible glmGamPoi dispersion-trend fits …
hyperpolymath Oct 18, 2026
01055c8
ci(fork): governance lane — DEED syntax and the Hypatia verdict grid …
hyperpolymath Oct 19, 2026
851e0dc
notes: how branches for upstream PRs get signed (#191)
hyperpolymath Oct 19, 2026
1e24eea
notes: re-sign a reviewed PR from its reviewed head; record the squas…
hyperpolymath Oct 20, 2026
98d1abb
feat(doi): add guarded Zenodo DOI publication (refs #8) (#195)
hyperpolymath Oct 22, 2026
2afcc1b
Validated exact and high-precision descriptive statistics (#1) (#199)
hyperpolymath Oct 22, 2026
a1fa3c7
feat(analysis): complete advanced zero handling (#197)
hyperpolymath Oct 22, 2026
f7ee0df
feat(evidence): Evidence Mode — claim editor, fibre & echo, residual …
hyperpolymath Oct 22, 2026
a1868d7
feat(analysis): multinomial and Dirichlet-multinomial differential ab…
hyperpolymath Oct 22, 2026
cb35704
feat(cladistics): add CladeCumulus ASV phylogenies (#200)
hyperpolymath Oct 22, 2026
4a1230a
fix: restore nullable config and DOI loading (#203)
hyperpolymath Oct 22, 2026
bb57baa
fix(doi): declare the DOI module that routes and tests already import…
hyperpolymath Oct 22, 2026
e313d97
Validated statistics API, persistence, and validation evidence (#1) (…
hyperpolymath Oct 22, 2026
fa4d213
feat(cladistics): CladeCumulus phylogenetic & epistemic integration (…
hyperpolymath Oct 22, 2026
9fe8178
feat(analysis): Advanced compositional methods — ANCOM-BC, ALDEx2, So…
hyperpolymath Oct 22, 2026
7bf8438
feat(analysis): add two-part count models and occupancy fitter (#196)
hyperpolymath Oct 22, 2026
c06c0d4
Fix frontend build and differential metadata regressions (#208)
hyperpolymath Oct 23, 2026
10a4a36
fix(analysis): restore differential method integrations (#211)
hyperpolymath Oct 23, 2026
c978994
Align high-precision fixtures with independent verifier (#213)
hyperpolymath Oct 23, 2026
a6e30fa
fix: load the package, and restore the docs and test registrations ma…
hyperpolymath Oct 23, 2026
8a37159
ci: surface and resolve remaining Julia test failures (#215)
hyperpolymath Oct 23, 2026
50a0e7f
Null-calibration bench + small-sample caveat (#193), with cross-PR in…
hyperpolymath Oct 23, 2026
7bb716d
fix(core): load the compositional models and unbreak the build tree (…
hyperpolymath Oct 23, 2026
9f4c944
refactor(frontend): remove the Evidence UI, keep the Evidence API (#7…
hyperpolymath Oct 23, 2026
a9b82e2
Fix validated-statistics run summaries 500 (invalid GROUP BY aggregat…
hyperpolymath Oct 23, 2026
8b76b71
Repair differential method union and frontend regressions (#210)
hyperpolymath Oct 23, 2026
8df1041
Fix CladeCumulus testset: field names, NHX capture, LWR tolerance, ro…
hyperpolymath Oct 23, 2026
87092cc
Land #217 (exact DuckDB counts) on main, and fix the Wald tail (#226)
hyperpolymath Oct 23, 2026
d337f74
fix: restore full 5,450-test CI green across CladeCumulus, compositio…
hyperpolymath Oct 23, 2026
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42 changes: 0 additions & 42 deletions .editorconfig

This file was deleted.

14 changes: 14 additions & 0 deletions .gitbot-fleet/enrolment.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
{
"schema": 1,
"reporters": {
"rhodibot": { "title": "rhodibot (RSR compliance)", "enrolled": true },
"panicbot": { "title": "panicbot (panic recovery, error handling)", "enrolled": true },
"echidnabot": { "title": "echidnabot (formal verification: proofs/)", "enrolled": true },
"seambot": { "title": "seambot (integration health: API routes)", "enrolled": true },
"finishingbot": { "title": "finishingbot (release readiness)", "enrolled": true },
"accessibilitybot": { "title": "accessibilitybot (WCAG on the React UI)", "enrolled": true },
"glambot": { "title": "glambot (presentation quality)", "enrolled": true },
"cipherbot": { "enrolled": false, "reason": "no cryptography is implemented in this repository" },
"sustainabot": { "enrolled": false, "reason": "fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)" }
}
}
83 changes: 0 additions & 83 deletions .github/CODE_OF_CONDUCT.md

This file was deleted.

89 changes: 0 additions & 89 deletions .github/SECURITY.md

This file was deleted.

53 changes: 0 additions & 53 deletions .github/dependabot.yml

This file was deleted.

48 changes: 12 additions & 36 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
@@ -1,43 +1,19 @@
## Summary
## Change and reason

<!-- What does this PR do, and why? One logical change per PR. -->
<!-- One logical change. Link relevant issues without claiming to close unrelated work. -->

Closes #
## Validation

## Type of change
<!-- Exact commands, results, and Julia/R/bun versions actually tested.
State explicitly what was not run. -->

- [ ] 🐛 Bug fix (non-breaking change that fixes an issue)
- [ ] ✨ New feature (non-breaking change that adds functionality)
- [ ] 💥 Breaking change (would change existing behaviour, a config key or an API response)
- [ ] 📊 Statistics fix (a method returned a wrong number, or a result it could not support)
- [ ] 📖 Documentation
- [ ] 🧹 Refactor / tech debt (behaviour-preserving)
- [ ] ⚡ Performance
- [ ] 🔧 Build / CI / tooling
## Scope

## How has this been verified?
<!-- What related work is left out? Explain any necessary lockfile change. -->

<!-- Name the commands you ran and what they reported. For example:
julia --project=. test/runtests.jl
julia --project=. -t 2 test/runtests.jl --integration --server
cd frontend && bun run test -->
## Contribution checks

Tested with Julia `…`, R `…` and bun `…`.

## What this leaves out

<!-- Anything related that this PR does not do, and why. -->

## Checklist

- [ ] My branch starts at the current tip of `main` (`behind_by` is `0`; see CONTRIBUTING.md) and has no merge commits from `main`.
- [ ] I ran `julia --project=. test/runtests.jl` (and `cd frontend && bun run test` for frontend changes) and they pass.
- [ ] CI ran on this PR and passes.
- [ ] No generated or vendored files, and no lockfile change the work does not need (or the reason is given above).
- [ ] New code is AGPL-3.0, or MPL-2.0 with an SPDX identifier in each file I wrote. I left existing file headers, `LICENSE`, `CITATION.cff` and the licence and acknowledgement sections of `README.md` unchanged.
- [ ] Every number shown to a user is computed from their data. When a method cannot run it raises an explicit error.
- [ ] Docs are updated, and no claim in them overstates what the code does.

## Notes for reviewers

<!-- Anything that needs special attention, follow-up, or context. To be considered for authorship in CITATION.cff, say so here. -->
- [ ] I followed [CONTRIBUTING.md](../CONTRIBUTING.md).
- [ ] This branch starts at current upstream main and contains no merges from fork main.
- [ ] CI has run and passes.
- [ ] Existing licensing, citation and acknowledgement text is unchanged.
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