From f868e143da4e1a0289fed00189da7998c67624aa Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 9 Apr 2026 15:36:18 +0000 Subject: [PATCH] chore: reorganize repo into proper directory structure per REPO_STRUCTURE.md Agent-Logs-Url: https://github.com/merrypranxter/reaction_diffusion/sessions/0cf7acfd-d2da-4316-a318-2bbc9d1e12e6 Co-authored-by: merrypranxter <159569959+merrypranxter@users.noreply.github.com> --- github-workflows_ci.yml => .github/workflows/ci.yml | 0 core__init__.py => core/__init__.py | 0 core_gray_scott.py => core/gray_scott.py | 0 core_laplacian.py => core/laplacian.py | 0 core_parameters.py => core/parameters.py | 0 core_seeding.py => core/seeding.py | 0 cpu__init__.py => cpu/__init__.py | 0 .../benchmarks/benchmark_results.md | 0 cpu_cython_accelerated.pyx => cpu/cython_accelerated.pyx | 0 cpu_fortran_backend.f90 => cpu/fortran_backend.f90 | 0 cpu_numpy_vectorized.py => cpu/numpy_vectorized.py | 0 .../01-mathematical-foundations.md | 0 .../02-gray-scott-deep-dive.md | 0 .../03-pearson-classification.md | 0 04-bifurcation-theory.md => docs/04-bifurcation-theory.md | 0 .../05-topological-defects.md | 0 .../06-implementation-patterns.md | 0 .../07-coloring-strategies.md | 0 .../08-spatial-parameter-sweeps.md | 0 09-alternative-models.md => docs/09-alternative-models.md | 0 .../10-blur-sharpen-equivalence.md | 0 .../threejs-webgl/index.html | 0 gpu__init__.py => gpu/__init__.py | 0 gpu_speedups.md => gpu/benchmarks/gpu_speedups.md | 0 gpu/pytorch/__init__.py | 7 +++++++ gpu_gray_scott_torch.py => gpu/pytorch/gray_scott_torch.py | 0 gpu_pearson_plot_gpu.py => gpu/pytorch/pearson_plot_gpu.py | 0 webgpu_compute.wgsl => gpu/webgpu/compute.wgsl | 0 webgpu_pipeline.js => gpu/webgpu/pipeline.js | 0 models__init__.py => models/__init__.py | 0 .../belousov_zhabotinsky.py | 0 model_cahn_hilliard.py => models/cahn_hilliard.py | 0 model_fitzHugh_nagumo.py => models/fitzHugh_nagumo.py | 0 model_schnakenberg.py => models/schnakenberg.py | 0 presets__init__.py => presets/__init__.py | 0 .../named-behaviors.json | 0 preset_pearson-types.json => presets/pearson-types.json | 0 shaders__init__.py => shaders/__init__.py | 0 shader_color-ramps.glsl => shaders/color-ramps.glsl | 0 shader_display-munafo.frag => shaders/display-munafo.frag | 0 shader_gray-scott-sim.frag => shaders/gray-scott-sim.frag | 0 tests__init__.py => tests/__init__.py | 0 test_convergence.py => tests/test_convergence.py | 0 test_laplacian.py => tests/test_laplacian.py | 0 test_presets.py => tests/test_presets.py | 0 tools__init__.py => tools/__init__.py | 0 tool_parameter_scanner.py => tools/parameter_scanner.py | 0 tool_profiler.py => tools/profiler.py | 0 tool_video_generator.py => tools/video_generator.py | 0 49 files changed, 7 insertions(+) rename github-workflows_ci.yml => .github/workflows/ci.yml (100%) rename core__init__.py => core/__init__.py (100%) rename core_gray_scott.py => core/gray_scott.py (100%) rename core_laplacian.py => core/laplacian.py (100%) rename core_parameters.py => core/parameters.py (100%) rename core_seeding.py => core/seeding.py (100%) rename cpu__init__.py => cpu/__init__.py (100%) rename benchmark_results.md => cpu/benchmarks/benchmark_results.md (100%) rename cpu_cython_accelerated.pyx => cpu/cython_accelerated.pyx (100%) rename cpu_fortran_backend.f90 => cpu/fortran_backend.f90 (100%) rename cpu_numpy_vectorized.py => cpu/numpy_vectorized.py (100%) rename 01-mathematical-foundations.md => docs/01-mathematical-foundations.md (100%) rename 02-gray-scott-deep-dive.md => docs/02-gray-scott-deep-dive.md (100%) rename 03-pearson-classification.md => docs/03-pearson-classification.md (100%) rename 04-bifurcation-theory.md => docs/04-bifurcation-theory.md (100%) rename 05-topological-defects.md => docs/05-topological-defects.md (100%) rename 06-implementation-patterns.md => docs/06-implementation-patterns.md (100%) rename 07-coloring-strategies.md => 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b/docs/08-spatial-parameter-sweeps.md similarity index 100% rename from 08-spatial-parameter-sweeps.md rename to docs/08-spatial-parameter-sweeps.md diff --git a/09-alternative-models.md b/docs/09-alternative-models.md similarity index 100% rename from 09-alternative-models.md rename to docs/09-alternative-models.md diff --git a/10-blur-sharpen-equivalence.md b/docs/10-blur-sharpen-equivalence.md similarity index 100% rename from 10-blur-sharpen-equivalence.md rename to docs/10-blur-sharpen-equivalence.md diff --git a/example_threejs-webgl.html b/examples/threejs-webgl/index.html similarity index 100% rename from example_threejs-webgl.html rename to examples/threejs-webgl/index.html diff --git a/gpu__init__.py b/gpu/__init__.py similarity index 100% rename from gpu__init__.py rename to gpu/__init__.py diff --git a/gpu_speedups.md b/gpu/benchmarks/gpu_speedups.md similarity index 100% rename from gpu_speedups.md rename to gpu/benchmarks/gpu_speedups.md diff --git a/gpu/pytorch/__init__.py b/gpu/pytorch/__init__.py new file mode 100644 index 0000000..77199a5 --- /dev/null +++ b/gpu/pytorch/__init__.py @@ -0,0 +1,7 @@ +""" +PyTorch GPU implementations for Gray-Scott reaction-diffusion. +""" +from .gray_scott_torch import GrayScottTorch +from .pearson_plot_gpu import PearsonPlotGPU + +__all__ = ['GrayScottTorch', 'PearsonPlotGPU'] diff --git a/gpu_gray_scott_torch.py b/gpu/pytorch/gray_scott_torch.py similarity index 100% rename from gpu_gray_scott_torch.py rename to gpu/pytorch/gray_scott_torch.py diff --git a/gpu_pearson_plot_gpu.py b/gpu/pytorch/pearson_plot_gpu.py similarity index 100% rename from gpu_pearson_plot_gpu.py rename to gpu/pytorch/pearson_plot_gpu.py diff --git a/webgpu_compute.wgsl b/gpu/webgpu/compute.wgsl similarity index 100% rename from webgpu_compute.wgsl rename to gpu/webgpu/compute.wgsl diff --git a/webgpu_pipeline.js b/gpu/webgpu/pipeline.js similarity index 100% rename from webgpu_pipeline.js rename to gpu/webgpu/pipeline.js diff --git a/models__init__.py b/models/__init__.py similarity index 100% rename from models__init__.py rename to models/__init__.py diff --git a/model_belousov_zhabotinsky.py b/models/belousov_zhabotinsky.py similarity index 100% rename from model_belousov_zhabotinsky.py rename to models/belousov_zhabotinsky.py diff --git a/model_cahn_hilliard.py b/models/cahn_hilliard.py similarity index 100% rename from model_cahn_hilliard.py rename to models/cahn_hilliard.py diff --git a/model_fitzHugh_nagumo.py b/models/fitzHugh_nagumo.py similarity index 100% rename from model_fitzHugh_nagumo.py rename to models/fitzHugh_nagumo.py diff --git a/model_schnakenberg.py b/models/schnakenberg.py similarity index 100% rename from model_schnakenberg.py rename to models/schnakenberg.py diff --git a/presets__init__.py b/presets/__init__.py similarity index 100% rename from presets__init__.py rename to presets/__init__.py diff --git a/preset_named-behaviors.json 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rename from tests__init__.py rename to tests/__init__.py diff --git a/test_convergence.py b/tests/test_convergence.py similarity index 100% rename from test_convergence.py rename to tests/test_convergence.py diff --git a/test_laplacian.py b/tests/test_laplacian.py similarity index 100% rename from test_laplacian.py rename to tests/test_laplacian.py diff --git a/test_presets.py b/tests/test_presets.py similarity index 100% rename from test_presets.py rename to tests/test_presets.py diff --git a/tools__init__.py b/tools/__init__.py similarity index 100% rename from tools__init__.py rename to tools/__init__.py diff --git a/tool_parameter_scanner.py b/tools/parameter_scanner.py similarity index 100% rename from tool_parameter_scanner.py rename to tools/parameter_scanner.py diff --git a/tool_profiler.py b/tools/profiler.py similarity index 100% rename from tool_profiler.py rename to tools/profiler.py diff --git a/tool_video_generator.py b/tools/video_generator.py similarity index 100% rename from tool_video_generator.py rename to tools/video_generator.py