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Pulling in recent changes from vraow
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After DD001 added the 8-phase predict→reference→inspect→refine→ implement→tune→render→compare methodology (commit dac96b7), extract analogous methodology sections into the four DDs whose subsystems share the same validation-shape concern. Each DD's methodology is adapted to its domain's lived references and tooling, but all follow the same horizontal pattern and produce the same MoaW-checklist / common-gotchas artifacts. DD010 (Validation Framework) — the meta-template: - New "Validation Workflow Pattern" section after Three-Tier table - Articulates the 8-phase pattern as the cross-tier meta-template - Shows how Tier 1, Tier 2, Tier 3 each instantiate the pattern (one phase-table column per tier) - Per-tier artifact requirements table - 7 anti-patterns MoaW flags (skip prediction, hand-sweep, post-hoc thresholds, etc.) - Points at DD001 as the canonical worked example - Quality Criteria #5: workflow-pattern-followed becomes binding - Quick Action Reference adds "Workflow pattern" row DD002 (Neural Circuit) — per-cell/per-pair/per-network methodology: - New "Validation Methodology" section (~100 lines) - Renames existing "Validation Procedure" → "Validation Procedure (Quick Reference)" to keep its bash one-liners separate from the deeper methodology - 4 levels: per-cell electrophysiology, per-synapse, per-network functional correlations, round-trip with body via Sibernetic - Each level has its own 8-phase table with the relevant reference datasets (Goodman 2002, Randi 2023, Yemini 2013) and acceptance thresholds - Expression-consistency shortcut for the ~121 neuron classes without patch-clamp data - 10-item MoaW PR review checklist (neural-circuit-specific) - 5 common gotchas (don't confuse prediction with simulation output, don't break network when tuning cells, don't add edges to Cook 2019 topology, etc.) - Forward-reference to differentiable substrate (DD001) for joint neural↔body fitting once neural ODE side gains differentiability DD003 (Muscle Model) — twitch/curves/round-trip methodology: - New "Validation Methodology" section (~95 lines) - Renames existing "Testing Procedure" → "Testing Procedure (Quick Reference)" - 3 levels: twitch dynamics (calcium→force pulse shape against Boyle & Cohen 2008), force-velocity/force-length curves (Hill 1938, Gordon-Huxley-Julian 1966), round-trip body bend - Round-trip level explicitly uses DD001's tooling (dump_metal_ trajectory.py, side-by-side render) - 10-item MoaW PR review checklist (muscle-model-specific) - 5 common gotchas (don't copy neuron HH params to muscle, don't skip Level 3 for "internal" changes, etc.) DD011 (Simulation Stack) — integration-layer methodology: - New "Stack Integration Validation Methodology" section (~90 lines) - Distinguishes integration-layer concern from scientific-accuracy concern: "does the plumbing keep working when the science changes?" - Two-Gate Model: quick-test (<5 min, no-crash) vs validate (<2 hr, DD010 tier gates); explicit "what each gate proves / does NOT prove" table - 8-phase methodology adapted to Docker / compose / orchestrator concerns - Subsystem-Onboarding Workflow (7 numbered steps for adding a new subsystem to the stack) - 10-item MoaW PR review checklist (integration-layer-specific) - 8 common gotchas (Dockerfile layer ordering, transitive deps, quick-test vs validate confusion, versions.lock drift, etc.) - Cross-DD Validation Coordination table — defines which DD owns which validation layer, with the Integration Maintainer as cross-DD arbiter when validators conflict Build verified: mkdocs build succeeds with zero new broken links. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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