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🏛️ Architect: Refactor Morphogenesis Stencil Logic #361

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🏛️ Architect: Refactor Morphogenesis Stencil Logic #361

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70efa72
Refactor morphogenesis to use Stencil Strategy Pattern
google-labs-jules[bot] Jan 27, 2026
d543b19
Apply cargo fmt fixes
google-labs-jules[bot] Jan 27, 2026
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5 changes: 5 additions & 0 deletions .jules/architect.md
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**Problem:** `math_explorer/src/biology/morphogenesis.rs` implemented a custom solver loop inside `TuringSystem::step`, preventing the use of generic ODE solvers (like Runge-Kutta 4) and duplicating integration logic. The state `TuringState` lacked standard arithmetic operators, making it incompatible with the library's `OdeSystem` ecosystem.
**Decision:** Applied "Traitification". Implemented `VectorOperations`, `OdeSystem`, and `TimeStepper` for `TuringSystem`. Preserved the highly optimized sliding-window stencil logic in `derivative_in_place` and the manual Euler step in `step`.
**Consequence:** `TuringSystem` is now a first-class citizen in the generic analysis module. It can be simulated with any `Solver` while maintaining zero-cost abstraction for the default use case.

## 2026-06-25 - [Reaction-Diffusion Stencil Abstraction]
**Problem:** `math_explorer/src/biology/morphogenesis.rs` contained duplicated logic for the finite-difference Laplacian stencil and sliding-window optimization in both `step` (Euler integration) and `derivative_in_place` (ODE derivative). This violated DRY and increased maintenance burden.
**Decision:** Refactored `morphogenesis` into a submodule. Extracted `Kinetics` and `State`. Implemented a generic `apply_reaction_diffusion_stencil` method using the "Closure Strategy". This method encapsulates the stencil math and optimization, accepting a closure to handle the result (either updating state or writing derivative).
**Consequence:** Code duplication eliminated. Logic for the optimized 1D stencil exists in exactly one place. The "Zero-Cost Abstraction" ensures no runtime penalty for the closure usage (monomorphization).
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