Reorganize flat-file repo into proper package directory structure

[Copilot]

All source files were dumped flat in the repo root with prefixed names (e.g. core_gray_scott.py, gpu_pearson_plot_gpu.py) instead of the intended subdirectory layout already documented in REPO_STRUCTURE.md.

Changes

• docs/ — 10 numbered theory/reference markdown files
• core/ — Gray-Scott engine, Laplacian operators, parameters, seeding
• cpu/ — NumPy, Cython, Fortran backends; benchmarks in cpu/benchmarks/
• gpu/pytorch/ — PyTorch CUDA impl + Pearson plotter; added missing __init__.py (required by gpu/__init__.py's relative imports)
• gpu/webgpu/ — WGSL compute shader + JS pipeline
• gpu/benchmarks/ — speedup results
• models/ — BZ, FitzHugh-Nagumo, Cahn-Hilliard, Schnakenberg
• shaders/ — GLSL/FRAG files
• presets/ — Pearson-types and named-behaviors JSON
• tests/ — convergence, Laplacian, and preset test suites
• tools/ — parameter scanner, video generator, profiler CLIs
• examples/threejs-webgl/ — interactive WebGL demo (index.html)
• .github/workflows/ — CI workflow

All moves done via git mv to preserve history. No file contents modified except the new gpu/pytorch/__init__.py.

[Copilot]

Pull request overview

This PR reorganizes the repository into a proper Python package/module directory structure (core/cpu/gpu/models/tools/tests/etc.) and adds supporting assets (presets, shaders, docs, examples) plus CI configuration to make the project testable/installable.

Changes:

• Introduces structured Python packages for core simulation, CPU/GPU backends, models, and tooling (plus __init__.py files).
• Adds presets, shader sources, documentation notes, and a Three.js WebGL example.
• Adds a GitHub Actions CI workflow to run formatting/type-check/tests and build wheels.

Reviewed changes

Copilot reviewed 1 out of 49 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tools/video_generator.py	CLI to generate an MP4 from a Gray-Scott run.
tools/profiler.py	CLI-ish utility to profile NumPy vs PyTorch implementations and emit a report.
tools/parameter_scanner.py	CLI to batch-render Pearson types and sweep (F,k) grids.
tools/init.py	Marks tools as a package.
tests/test_presets.py	Validates preset JSON structure/content.
tests/test_laplacian.py	Laplacian operator unit tests and equivalence checks.
tests/test_convergence.py	Numerical stability/pattern/convergence tests for the simulator.
tests/init.py	Marks tests as a package.
shaders/gray-scott-sim.frag	WebGL fragment shader implementing Gray-Scott step.
shaders/display-munafo.frag	WebGL fragment shader for Munafo-style visualization.
shaders/color-ramps.glsl	Shared GLSL color ramp utilities.
shaders/init.py	Marks shaders as a package.
presets/pearson-types.json	Pearson-type parameter presets for Gray-Scott.
presets/named-behaviors.json	Named (F,k) behaviors presets.
presets/init.py	Marks presets as a package.
models/schnakenberg.py	Schnakenberg model implementation.
models/fitzHugh_nagumo.py	FitzHugh–Nagumo model implementations (grid + network).
models/cahn_hilliard.py	Cahn–Hilliard spectral solver + noisy variant.
models/belousov_zhabotinsky.py	BZ/Oregonator and simplified excitable-medium model.
models/init.py	Exports models package surface (__all__).
gpu/webgpu/pipeline.js	WebGPU compute pipeline orchestration (resources, uniforms, dispatch).
gpu/webgpu/compute.wgsl	WebGPU compute shader for Gray-Scott.
gpu/pytorch/pearson_plot_gpu.py	PyTorch Pearson-plot (spatial parameter sweep) implementation.
gpu/pytorch/gray_scott_torch.py	PyTorch Gray-Scott implementation using conv2d Laplacian.
gpu/pytorch/init.py	Exposes PyTorch GPU implementations as a subpackage.
gpu/benchmarks/gpu_speedups.md	Documentation of observed GPU speedups.
gpu/init.py	Top-level GPU package import shim / optional exports.
cpu/numpy_vectorized.py	Vectorized NumPy Gray-Scott baseline implementation.
cpu/cython_accelerated.pyx	Cython-accelerated stepping implementation + wrapper class.
cpu/fortran_backend.f90	Fortran backend routines (f2py target).
cpu/benchmarks/benchmark_results.md	CPU benchmark result write-up.
cpu/init.py	CPU package exports and optional Cython import.
core/seeding.py	Seed/initial-condition generators for simulations.
core/parameters.py	Dataclasses + canonical parameter presets (Pearson types, named behaviors).
core/laplacian.py	Laplacian kernels and implementations (5-pt, 9-pt, convolution).
core/gray_scott.py	Core NumPy Gray-Scott simulator + image/state helpers.
core/init.py	Core package exports and public API surface.
docs/01-mathematical-foundations.md	Theory reference: reaction-diffusion basics, Laplacians, stability.
docs/02-gray-scott-deep-dive.md	Theory reference: Gray-Scott equations, seeding, parameters.
docs/03-pearson-classification.md	Theory reference: Pearson taxonomy and parameter map.
docs/04-bifurcation-theory.md	Theory reference: bifurcation boundaries and implications.
docs/05-topological-defects.md	Theory reference: defect types and shader injection ideas.
docs/06-implementation-patterns.md	Reference on CPU/GPU implementations and kernels.
docs/07-coloring-strategies.md	Reference on visualization/coloring strategies.
docs/08-spatial-parameter-sweeps.md	Reference on Pearson plots/spatial parameter sweeps.
docs/09-alternative-models.md	Overview of alternative models included in models/.
docs/10-blur-sharpen-equivalence.md	Reference on blur+unsharp-mask equivalence to RD.
examples/threejs-webgl/index.html	Browser demo: Gray-Scott simulation via Three.js/WebGL.
.github/workflows/ci.yml	CI pipeline for lint/typecheck/tests/coverage + wheel builds + benchmarks.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.