Feature/divergence

[wwang721]

Close #8 now by setting a small cutoff $\delta$ to regulate the singularity.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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[Copilot]

Pull request overview

This pull request addresses issue #8 by introducing a delta parameter to regulate singularities in force calculations when cells are very close together. The PR includes significant code reorganization, splitting the monolithic finite_voronoi.py into separate modules for better maintainability, and adds new functionality to compute optimal delta values based on target forces.

Key changes:

• Added delta parameter to PhysicalParams with helper methods (with_delta, with_optimal_radius) and a new target_delta function to compute delta from target forces
• Applied singularity fix in force calculations using np.maximum(root[:, None], self.phys.delta) in both fast and fallback implementations
• Restructured codebase into backend.py, simulator.py, and physical_params.py for cleaner separation of concerns

Reviewed changes

Copilot reviewed 16 out of 17 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
afv/__init__.py	New file defining the public API with version 0.2.4, exports PhysicalParams, FiniteVoronoiSimulator, and target_delta
afv/backend.py	New file implementing backend selection logic (Cython vs Python fallback)
afv/simulator.py	New file providing the API-facing FiniteVoronoiSimulator wrapper with backend detection and fallback warnings
afv/physical_params.py	New file containing PhysicalParams dataclass with delta parameter, optimization methods, and target_delta function
afv/finite_voronoi.py	Removed (functionality split into new modules)
afv/finite_voronoi_fast.py	Updated to import PhysicalParams from new module and apply singularity fix with delta
afv/finite_voronoi_fallback.py	Updated to import PhysicalParams from new module, apply singularity fix, and remove trailing whitespace
tests/conftest.py	Updated to use new import pattern, added delta=0.45 to test fixture, parameterized simulator fixture for both backends
tests/test_core.py	Added delta handling in MATLAB test and new test_physical_params function to validate delta computations
tests/test_geom.py	Added test case for N=2 separated points and improved comment clarity for collinear case
examples/relaxation.py	Updated imports to use new import afv pattern
examples/connections.py	Updated imports to use new import afv pattern
examples/active_FV.py	Updated imports to use new import afv pattern
examples/jupyter/custom_plot.ipynb	Updated imports, improved line wrapping in comments, updated execution timestamps
pyproject.toml	Version bumped from 0.2.2 to 0.2.4
README.md	Updated badge URLs to feature branch, updated import examples, clarified fallback behavior notes, updated issue status

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