docs: refresh README + CONTRIBUTING for current project state - #202
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Both files were last updated 2026-04-18, ~633 commits and 5 brain architectures behind the current codebase. Reconcile against the @register_brain registry and AGENTS.md. README.md: - Brain count 19 -> 24; add equivariantquantum, cfcppo, feedforwardga, spikingppo, connectomeppo to their categories - Features: add evolutionary optimization & inheritance, connectome substrate, pluggable architecture interface - Roadmap: move Evolution & Breeding to Recently Completed (Phase 5 done), promote connectome substrate to in-progress, refresh help-wanted CONTRIBUTING.md: - Brain count 19 -> 24 (renumbered across categories) - Testing tiers three -> four (add slow tier; correct pre-commit subset vs full-suite commands) - Rewrite "Adding a New Brain Architecture" for the @register_brain plug-in registry; link plugin-developer-guide.md - Logbook index example 008 -> 026; add new evolution/analysis scripts docs/roadmap.md: - One stale "19 brain architectures" line -> 24; add GA-evolved and connectome-constrained families Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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📝 WalkthroughWalkthroughThis PR updates project docs to reflect 24 brain architectures (added EquivariantQuantumPPOBrain), reorganizes test guidance into four tiers, replaces the "Adding New Features" flow with a plugin/registry workflow, extends experiment logbook examples, and expands README/roadmap feature and roadmap items. ChangesDocumentation Updates
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chrisjz
marked this pull request as ready for review
June 4, 2026 09:46
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Inline comments:
In `@README.md`:
- Line 26: The README shows "Connectome Substrate" as shipped (the line with "✅
**Connectome Substrate**: Connectome-constrained brains...") but also lists it
as in-progress in the Roadmap; pick one status and make both sections
consistent. Update the Features entry and the Roadmap entry for the "Connectome
Substrate" string so they use the same status wording/icon (e.g., change the
Features line to "In progress/Partial — Connectome Substrate..." or change the
Roadmap to mark it as shipped) and ensure the descriptive text (Cook et al.
2019, 302 neurons...) remains identical across both places to avoid divergence.
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CONTRIBUTING.mdREADME.mddocs/roadmap.md
| - ✅ **Classical ML Alternatives**: REINFORCE, PPO, DQN, LSTM/GRU PPO, and spiking neural network brain architectures | ||
| - ✅ **Quantum Learning**: Parameter-shift rule for gradient-based optimization | ||
| - ✅ **Evolutionary Optimization & Inheritance**: CMA-ES, genetic algorithms, and TPE hyperparameter search, plus Lamarckian weight inheritance, Baldwin-effect, and predator-prey co-evolution | ||
| - ✅ **Connectome Substrate**: Connectome-constrained brains on the real *C. elegans* wiring diagram (302 neurons, Cook et al. 2019) with chemical synapses and gap junctions |
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Unify Connectome Substrate status across sections.
README currently presents Connectome Substrate as both shipped (✅ in Features) and in-progress (Roadmap), which creates conflicting guidance for contributors. Pick one status model (e.g., “partial/in-progress” in both places) and apply consistently.
Also applies to: 393-393
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@README.md` at line 26, The README shows "Connectome Substrate" as shipped
(the line with "✅ **Connectome Substrate**: Connectome-constrained brains...")
but also lists it as in-progress in the Roadmap; pick one status and make both
sections consistent. Update the Features entry and the Roadmap entry for the
"Connectome Substrate" string so they use the same status wording/icon (e.g.,
change the Features line to "In progress/Partial — Connectome Substrate..." or
change the Roadmap to mark it as shipped) and ensure the descriptive text (Cook
et al. 2019, 302 neurons...) remains identical across both places to avoid
divergence.
The Features list marked "Connectome Substrate" ✅ (shipped — connectomeppo is a registered, runnable brain) while the Roadmap reused the identical label as "(in progress)". Rename the Roadmap entry to "Connectome Architecture Comparison" so it names the actually-open Phase 6 work (closed-loop learning/evolution + NEAT ranking) per roadmap.md, removing the same-label contradiction. Shared "302 neurons, Cook et al. 2019" descriptor stays identical across both. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
README.md and CONTRIBUTING.md were last updated 2026-04-18 — ~633 commits and 5 brain architectures behind the current codebase. This reconciles them (plus one stale line in
docs/roadmap.md) against the@register_brainregistry and AGENTS.md.Changes
README.md
equivariantquantum,cfcppo,feedforwardga,spikingppo,connectomeppoto their categoriesCONTRIBUTING.md
slowtier; corrected pre-commit subset vs. full-suite commands)@register_brainplug-in registry; links the Plugin Developer Guidedocs/roadmap.md
Verification
pre-commit run --files(mdformat + markdownlint-cli2) passesBrainTypeenum members, registrynamematches, import paths in the example, test commands, script descriptions, logbook filenames, and the plugin-guide link target verified against the codebaseReviewer note
Minor consistency point (not blocking): "Connectome Substrate" appears as ✅ in the Features list (capability shipped) and "(in progress)" in the roadmap (Phase 6 arc open) — different senses of the same label. Left as-is pending preference on wording.
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