Use contiguous memory layout for neighbor lists

[efaulhaber]

Based on #111.

[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.78%. Comparing base (d3472d2) to head (7d639e4).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/nhs_precomputed.jl	78.78%	7 Missing ⚠️
src/gpu.jl	0.00%	6 Missing ⚠️
src/neighborhood_search.jl	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #10      +/-   ##
==========================================
- Coverage   86.96%   84.78%   -2.19%     
==========================================
  Files          15       15              
  Lines         660      690      +30     
==========================================
+ Hits          574      585      +11     
- Misses         86      105      +19     

Flag	Coverage Δ
unit	84.78% <66.66%> (-2.19%)	⬇️

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[Copilot]

Pull Request Overview

This PR adds support for using Vector{Vector} as a backend for PrecomputedNeighborhoodSearch, making it more flexible and memory-efficient for certain use cases. It also introduces a freeze_neighborhood_search function to strip unnecessary data structures when preparing neighborhood searches for GPU execution.

• Refactored PrecomputedNeighborhoodSearch to support configurable backends (DynamicVectorOfVectors or Vector{Vector})
• Added freeze_neighborhood_search to optimize GPU transfers by removing internal neighborhood searches
• Introduced max_inner_length helper function to handle backend-specific configuration copying

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/nhs_precomputed.jl	Refactored struct to support configurable backends, added freeze_neighborhood_search implementation
src/vector_of_vectors.jl	Added max_inner_length helper for extracting backend configuration
src/neighborhood_search.jl	Added generic freeze_neighborhood_search interface
src/gpu.jl	Updated GPU adaptation to handle PrecomputedNeighborhoodSearch instead of GridNeighborhoodSearch
src/cell_lists/spatial_hashing.jl	Fixed trailing whitespace in documentation
src/cell_lists/full_grid.jl	Updated documentation and replaced max_points_per_cell with max_inner_length
benchmarks/smoothed_particle_hydrodynamics.jl	Added freeze_neighborhood_search call before GPU transfer
benchmarks/n_body.jl	Added freeze_neighborhood_search call before GPU transfer
benchmarks/run_benchmarks.jl	Added PrecomputedNeighborhoodSearch to GPU benchmark suite
test/neighborhood_search.jl	Added test cases for PrecomputedNeighborhoodSearch with Vector{Vector} backend

Comments suppressed due to low confidence (1)

src/nhs_precomputed.jl:128

• The element type Int[] should be consistent with the backend type. When using Vector{Vector{Int32}} backend, this creates Vector{Int} elements instead of Vector{Int32}, which is inconsistent. Consider using the element type from the backend or making this type-stable.

        neighbor_lists[i] = Int[]

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