feat: improve diffusion geometry

.github/workflows/ci.yml

@@ -70,6 +70,7 @@ jobs:
           test_ops_spectral_geometry
           test_ops_hodge
           test_io_meshes
+          igneous-hodge
 
       - name: Run tests
         shell: bash
@@ -145,6 +146,7 @@ jobs:
           test_ops_spectral_geometry
           test_ops_hodge
           test_io_meshes
+          igneous-hodge
 
       - name: Run tests (Sanitizers)
         shell: bash

.gitignore

@@ -5,3 +5,8 @@
 .DS_Store
 __pycache__/
 *.pyc
+*.png
+DiffusionGeometry/
+notes/hodge/.venv_ref/
+notes/hodge/results/*
+!notes/hodge/results/.gitkeep

CMakeLists.txt

@@ -85,3 +85,14 @@ target_link_libraries(igneous-spectral PRIVATE igneous fmt::fmt)
 
 add_executable(igneous-hodge src/main_hodge.cpp)
 target_link_libraries(igneous-hodge PRIVATE igneous fmt::fmt)
+
+add_test(
+  NAME test_hodge_cli_outputs
+  COMMAND bash ${CMAKE_SOURCE_DIR}/tests/test_hodge_cli_outputs.sh
+          $<TARGET_FILE:igneous-hodge>)
+set_tests_properties(test_hodge_cli_outputs PROPERTIES LABELS "hodge;cli")
+
+add_test(
+  NAME test_hodge_parity_optional
+  COMMAND bash ${CMAKE_SOURCE_DIR}/tests/test_hodge_parity_optional.sh)
+set_tests_properties(test_hodge_parity_optional PROPERTIES LABELS "hodge;parity")

README.md

@@ -46,6 +46,30 @@ cmake --build build -j8
 ./build/igneous-hodge
 ```
 
+## Reference Implementation
+
+The diffusion/Hodge parity work in this repository is aligned against the Python
+reference implementation:
+
+- [DiffusionGeometry](https://github.com/Iolo-Jones/DiffusionGeometry)
+
+## Hodge Parity Workflow
+
+Standard parity round:
+
+```bash
+./scripts/hodge/run_parity_round.sh
+```
+
+Optional diagnostic plots for a parity round:
+
+```bash
+ROUND_DIR="$(ls -1dt notes/hodge/results/round_* | head -n1)"
+notes/hodge/.venv_ref/bin/python \
+  ./scripts/hodge/diagnostics/plot_hodge_outputs.py \
+  --round-dir "${ROUND_DIR}"
+```
+
 Set `IGNEOUS_BENCH_MODE=1` to disable heavy export paths in runtime apps.
 
 Runtime backend controls:
@@ -74,6 +98,8 @@ Current suites:
 - `test_ops_spectral_geometry`
 - `test_ops_hodge`
 - `test_io_meshes`
+- `test_hodge_cli_outputs`
+- `test_hodge_parity_optional` (skips unless `DiffusionGeometry/` is available, unless forced)
 
 ## Benchmarks
 

benches/bench_dod.cpp

@@ -83,7 +83,7 @@ static DiffusionMesh make_diffusion_cloud(size_t n_points) {
   }
 
   mesh.topology.build({mesh.geometry.x_span(), mesh.geometry.y_span(),
-                       mesh.geometry.z_span(), 0.05f, 32});
+                       mesh.geometry.z_span(), 32});
   return mesh;
 }
 
@@ -127,7 +127,7 @@ static void bench_diffusion_build(benchmark::State &state) {
 
   for (auto _ : state) {
     mesh.topology.build({mesh.geometry.x_span(), mesh.geometry.y_span(),
-                         mesh.geometry.z_span(), 0.05f, 32});
+                         mesh.geometry.z_span(), 32});
     benchmark::DoNotOptimize(mesh.topology.markov_values.size());
   }
 }

benches/bench_pipelines.cpp

@@ -83,9 +83,10 @@ int compute_max_y_vertex(const DiffusionMesh &mesh) {
   return max_y_idx;
 }
 
-void build_diffusion_topology(DiffusionMesh &mesh, float bandwidth, int k_neighbors) {
+void build_diffusion_topology(DiffusionMesh &mesh, float /*bandwidth*/,
+                              int k_neighbors) {
   mesh.topology.build({mesh.geometry.x_span(), mesh.geometry.y_span(),
-                       mesh.geometry.z_span(), bandwidth, k_neighbors});
+                       mesh.geometry.z_span(), k_neighbors});
 }
 
 void bench_pipeline_diffusion_main(benchmark::State &state) {