arborist/docs/_source
russell@unturf.com fd643fe1a5
#000012 Phase 1b: Merkle-AGI v8 consensus paper landed
`docs/_source/merkle-agi-v8-consensus.rst` (834 lines, RST sister
to the v7-W substrate paper at the same path). Closes Phase 1b of
ticket #000012 — the loop-closing consensus protocol that turns
single-validator Proof-of-Upgrade into Darwinian selection across
an open validator set.

11 parts:

  Part 1   Introduction & motivation — gap table from v7 § 13.4,
           concrete backdoor-attack scenario, paper IS/IS-NOT
           scope.
  Part 2   Substrate definition — SQD A1/A2/A3 inheritance,
           consensus_events row schema, consensus_policy_hash
           sibling (never enters cache_key).
  Part 3   Validator state machine — bonding/active/challenged/
           slashed/unbonding with full transition graph + invariants.
  Part 4   Acceptance protocol — proposer submission, layered
           fitness floor (canonical + lab-declared ceiling),
           audit-replay procedure, 2/3-stake quorum + GRANDPA-
           style finalization, liveness floor.
  Part 5   Challenge protocol — counter-evidence shape,
           adjudication, challenger reward, frivolous-challenge
           bond.
  Part 6   Stake mechanics — bond/unbond/challenge window
           recommendations, offense-class slashing schedule,
           reward distribution, optional stake cap + sqrt-weighting.
  Part 7   Fork choice rule — GRANDPA-style finality, pre-finality
           constraints, liveness recovery.
  Part 8   Mesh wire format extension — three new message kinds,
           BLS-or-concat aggregate signatures, bandwidth profile.
  Part 9   BFT analysis — safety, liveness, Sybil resistance,
           bootstrap honesty, re-staking attacks.
  Part 10  Worked example — 7-validator deployment, one upgrade
           cycle with successful challenge against one fraudulent
           validator.
  Part 11  Out of scope — implementation, calibration, cross-chain
           anchoring, fixture selection, bootstrap-set membership,
           cross-instance slashing accumulator, branch-set
           persistence.

Closure §: open questions tracked separately (initial validator
set composition, threshold-key ceremony, ZK-replay, policy-hash
transition mechanics).

Ticket #000012 status updated; Phase 1c (branch-set persistence)
remains proposed-not-opened. Implementation follow-up tickets that
cite this paper land later — one per validator-state-machine,
mesh-wire-format extension, audit-replay harness, slashing
accountant.
2026-05-10 16:12:00 -04:00
..
_ext docs: clear all 39 cold-build Sphinx warnings (truly green) 2026-05-09 18:00:15 -04:00
_static docs: add Read the Docs configuration 2026-05-04 08:17:24 -04:00
api docs: open ticket #000022 (adapter LossReport) + federation doc-discoverability fix 2026-05-07 16:36:13 -04:00
bench.rst CLI: arborist v8 score → arborist substrate score 2026-05-10 09:12:34 -04:00
concepts.rst docs: clear all 39 cold-build Sphinx warnings (truly green) 2026-05-09 18:00:15 -04:00
conf.py docs: footer attribution → russell@unturf./foxhop/TimeHexOn/legallydav1dpro unturf permacomputers 2026 2026-05-07 14:53:33 -04:00
cookbook.rst aborist/arborist 2026-05-07 09:31:49 -04:00
diagrams trim Makefile (-6 redundant targets) + better RTD docs 2026-05-04 09:03:03 -04:00
index.rst docs: clear all 39 cold-build Sphinx warnings (truly green) 2026-05-09 18:00:15 -04:00
license.rst aborist/arborist 2026-05-07 09:31:49 -04:00
Makefile docs: add Sphinx API reference generation from docstrings 2026-05-04 07:55:34 -04:00
merkle-agi-v7w-spatial-temporal.rst docs: clear all 39 cold-build Sphinx warnings (truly green) 2026-05-09 18:00:15 -04:00
merkle-agi-v8-consensus.rst #000012 Phase 1b: Merkle-AGI v8 consensus paper landed 2026-05-10 16:12:00 -04:00
pi-star.rst docs: propagate kernel/sub-battery counts to canonical surfaces 2026-05-09 17:27:02 -04:00
quickstart.rst aborist/arborist 2026-05-07 09:31:49 -04:00
README.md aborist/arborist 2026-05-07 09:31:49 -04:00
requirements.txt docs: switch to sphinx-book-theme for unified right-side project TOC 2026-05-04 09:13:14 -04:00
v8-fork-score.rst CLI: arborist v8 score → arborist substrate score 2026-05-10 09:12:34 -04:00

Arborist API Reference (Sphinx)

This directory contains Sphinx configuration to generate API documentation from docstrings.

Build

cd docs/_source
make html           # Generate HTML (output: _build/html/)
make text           # Generate text (output: _build/text/)
make clean          # Remove build artifacts

Or directly:

sphinx-build -b html . _build/html

View

After building, open _build/html/index.html in a browser.

Structure

  • conf.py — Sphinx configuration
  • index.rst — Main table of contents
  • api/ — Module documentation (one .rst per module category)
    • substrate.rst — Core data structures (merkle, document, wikitext)
    • storage.rst — SQLite schema (store, ingest, evict)
    • retrieval.rst — FTS5 search (search, sources, concepts)
    • qa.rst — Q&A pipeline (runner, query, verify, evidence, etc.)
    • distill.rst — Distillation (surface→core)
    • mesh.rst — Federation (gossip-based sync)
    • cli.rst — Command-line interface

What it replaces

This generated documentation replaces docs/modules.md (1200+ lines of static API reference). The docstrings in code are the source of truth; Sphinx extracts them automatically.

Adding new modules

  1. Add a docstring to the module (module-level docstring at the top of module.py)
  2. Add an .rst file in api/ that includes the module with automodule directive
  3. Reference it in index.rst
  4. Rebuild with make html

Theme

Uses furo theme (modern, responsive, search-enabled).

Autodoc directives

The .rst files use Sphinx automodule to extract:

  • Module docstrings
  • Class docstrings + members
  • Function signatures + docstrings
  • Source code links (:viewcode: extension)

See Sphinx autodoc docs.